-What are the limits of the stock birfields?Depends on your driving style. I have seen a club member go through one a year with 31" Swampers. I run 33x12.5" MT's with stock birfields and have only broken one in 4 years of wheeling. I have twisted the splines my front axles though, had to upgrade to heavy duty ones. Still stock birfs though. Until I get my new Trail Tough chromoly's.
-What kind of backspacing are you running on 30", 31" tires?Stock rims will work, but they tend to be a bit thin if your running wider tires as they are only 7" wide (I think). 3.5 seems to be a good number if your buying custom wheels. You can always just get a set of spacers.
-What production wheel had a similar design?Sammy's and Tracker/Sidekicks both use the 5 on 5.5" bolt pattern. Similar to Fords Half Tons, Jeep CJs, and International Scout according to Allied Tires web site.
-Are longer shackles and fender trimming enough for 30's?Depends on the 30's and your definition of fender trimming. I know you can squeeze 29" tires under a Samurai un-lifted if you trim the front bumper, so with some fender trimming and probably larger bump stops you should be ok.
-I've run around here looking for cheap/free mods and haven't found to many or any actually is there a faq that some one can link me to please. Acks Faq is a good place to start.
http://acksfaq.com/ As for mods, it's usually easier to just search for what you want to do with the search function. Then go through and look at how people have done it. Or just ask some questions and wait a few days for people to chime in with their answers.