This is everything I could gather and decipher concerning the site's reputation system.  If anyone has any additional insight on the rating system, please post below and I will include here, shamelessly taking full credit for your discovery (just kidding – full credit will be given).

The 4 Reputation Elements  (Connections, Value, Participation, and Skill) are a ranked list of all users.  Each element is relative to other users, listed by percentage.  The index is your position among all users - 68 means you are higher than 68% of the site members. 

This is why:
-Everyone active has a participation in the 90s – there are lots of zeros in the scale from people who have left the site.
-It is easy to get big reputation gains as a noobie (you are jumping over inactive users) but progress slows later (you are compared to people who post all of the time).
-It is hard to decipher – the scales are unknown, non-linear. and change daily.
-Many stall in the low 90s – there are a lot of people grouped in the range of 220-260, lots of inactive accounts below this.

Reputation Index  is the sum of the 4 reputation elements.  It is a comparison of your total against other users.  The index has a limit on the rate of increase for new accounts - the fastest a noobie can reach 99 is about 2 months from your initial comment.  The time limit does not start until you begin posting comments.

This scale changes daily.  Right now you need about 200 to be a Superstar, 350 to be in the top 1000.

You can get an estimate of the total you need to obtain a given reputation index.  Locate several users who have nearly constant values in their 4 elements and reputation for 2 months, and a reputation in the range you are targeting below 97.  Add up the total of their 4 elements and you have an idea of what total you need to be to achieve the same reputation!  Exceptions were discovered among people who had low value but high skill indexes – we could not determine what caused this.

1. Connections are the sum of the reputations of people who list you as a favorite member.  The more who list you as a favorite, the higher your connections index.  Being listed by someone with a low reputation will still improve your connections.  The site limits you to 150 people in your favorites, but you can exceed this as described in the blog linked to below:
How to Exceed the 150 Favorites Limit

To add some one as a favorite, go to their profile page and click on Add Favorite in the top right corner.  Page thru your connections regularly, adding anyone who lists you as a favorite (otherwise they will get annoyed and drop you as a favorite).  When you add someone as a favorite, be patient – it may be some time before they scan thru their favorites to return the favor.  (I usually give them at least a month).

Bloggers are good source of favorites (bloggers need love too).  They can still use a boost to maintain their reputation index, and having their blogs appear in the profile of others helps promote their hobby.  Be certain to leave a nice comment to attract their attention.

Check your "Reviews Of" in your profile.  If someone is reviewing a lot of your comments over time or are part of an ongoing discussion, they will probably reciprocate a favorites addition (you aren't just another Avatar).

Boost Your Connection/Favorites Threads provide a location where participants mutually add each other as a favorite.  If you start a thread some suggestions are in the 1^st comments of this blog.  If you start a thread in a new section or know of a thread not listed below, post the link below and I will add it to this list of existing threads:
Off Topic Boost your connections rating!!
College Football Boost your value today
MLB Add Value And Favorites To Your Profile

2. Value is the total of all ratings a user gets across all their content divided by the number of posts made by that user.  I believe the system goes back over all of the contents for the previous 30 days, but could be as long as 90.  You can rate comments up to 30 days old.

Rating  =  reputation of the reviewer (0-100)  x  rating (1-5)  x  scale  x  content weight

The scale is the average score the reviewer uses. Users that give everyone 5 stars will have their 5s worth 2.5 stars only. If you only value comments a 5, you might as well continue because the system will adjust whatever your rate to average 2.5 anyway – vsarying the rating won’t make a difference to the avrage score you give.

Getting a low score (1 star) will not drop your comment value (a 1 is still better than no rating).  Giving a low rating to troll comments will still boost the author's score.

Each type of content has a content weight - blogs have a content weight of 9 while messages have a weight of 5.

The site notes objectively rating others' content will help your reputation, rating content in a haphazard or contrary manner will hurt your reputation.  I have seen absolutely no evidence this is true – I suspect it is an attempt to discourage retaliatory scoring or value threads (viva la revolution!).

Comment Score is not part of the value calculation.  It is used for placement in the listings.  Achieving a high or low comment score has no effect on your value index.  It appears to be a function of the the author's reputaion, grammar (a series of exclamation marks drops the score), spelling, use of obscenities, paragraph foramtting (1 paragraph scores higher), and overall length.  Since it doesn't matter, I didn't break it down further.

For the hard core (noobs looking to boost their value while they build up their other elementsd and those looking to be in the Top 1000) find a group where they mutually agree to rate each other’s comments.  This involves going into their profile, viewing all of their comments, and rating every one a 5.  It is very effective, but it is time consuming.  If participants are in each other’s favorites, as their value (and reputation) goes up, your connections and reputation goes up as well.  This then boosts the connections and reputation of everyone who has you as a favorite, which then boosts your connections and reputation again.  The loop eventually dies out, but the impact increases the more common favorites there are in the group.

Boost your Value Threads provide a location where you post anything and everyone rates the comments a 5.  When you post go back at least 3 pages and hand out 5s to everyone else.  If you plan to participate heavily for a while, go back and rate every comment in the thread (you can go back 1 month).  If you plan to make a LOT of comments, spread yourself out among the different threads rather than create lots of comments in a single thread – it can take a long time for participants to rate every comment in a single thread.  If you start a thread in a new section of the site, post below and I will add it to this list of existing threads:
NCAABB NCAA BB Fives
College Football Boost your value today
College Football Looking To Boost Value???
Off Topic Boost you Value rating!!!
MLB Add Value And Favorites To Your Profile

3. Participation is so easy to get I didn’t bother to try to figure out its details.  Doing just about anything that leaves a foot print counts toward participation.  I think it is more related to how often you comment than many comments you leave.  So many accounts have been started and abandoned it doesn’t take a lot of effort to get participation in the 90s.

If you are busy or returning after an extended leave, I recommend posting in the “Boost Your Value” threads.

4. Skills are based on fantasy games.  Points are awarded at the end of the season, so they are a better tool for vets wanting to keep access rights than noobs.

Set up some fantasy teams in every free game if you followe the sport to see if you can get some easy points.  Even if you don't follow the football, NCAAF and BFL is very easy (I won the regular season with my fantasy NFL team even though I didn't watch a total of 10 minutes of NFL games all season!)  On the other hand, NBA and NHL is a bit more complicated so I abandoned these teams.

To access these, click on fantasy in the top left of the screen.  The site has an auto draft feature for fantasy teams used by some leagues, so you don’t have to know anything to participate – enter or start a rookie league that uses auto draft, set your starting roster, then you can forget about it.

The Top 1000 is a distinction for those with the highest total of all 4 categories – you will need to do well in all to make this level.   Last I checked, the threshold looks to be around a total of over 350.

I would suggest:  Max out connections and participation to 99 with the above hints including the procedure for exceeding the 150 favorites limit.  Max out value by joining with noobs to mutually value each others comments.  Take part in Boost Your Value threads.  Skill is no longer an option – if fantasy teams aren’t your thing, look for a rookie league to join, and follow the bloggers who give advice as their hobby.
Consider starting a 2nd account for commenting in threads and blogs since comments that do not receive a 5 star rating drop your vale index - you can make the new account identical to the old except for a minor change in the name spelling, and can even note it is a 2nd account profile so others know it is you.

Warnings and Reports limit your Reputation index if they are found valid, otherwise they make no difference.  If you are a superstar, 1 waring limits your reputation index to 94 (All Star), 3 limits you to 79 (Pro), 6 limits you to 49 (Amateur), and 9 limits you to 24 (Rookie) for 3 months.  No matter what you do, you cannot shorten this time span or get above the limit.  On the 1st day you drop to 0, but on the 2nd day it return to the new limit.  Making too many reports can result in your account being limited, but i do not know what the limit is. 

References
CBSSports.com redesign comments and answers
My Value is Going Down 
Rating Changes Effective Tomorrow
XxBronxBomberxX helped me crack the reputation threshold totals
C.Coolidge1933 detailed the warnings and reports penalty
orangemen90 helped me sort fact from "Urban Legend"
R.W. Chan is an administrator who verified the value rating system
dAdXeR is an administrator who helped with the comment score use