In order to take advantage of E85 the engine must be built to a high compression ratio. Some good info I've found on E85 for performance:
http://members.tccoa.com/392bird/e85.htm
FrankZ and 1bolt seem to know the most about this. FrankZ for his interest and later unsuccessful use of E85 and 1bolt for his interest in a high compression build.
First a conversion kit is necessary to adjust the A/F ratio, available sources are:
http://www.fullflexint.com/
http://etechmn.com/
http://www.change2e85.com/ - I've read somewhere that this automatically adjust the A/F ratio based on fuel blend, can anyone confirm this?
http://www.e85conversionkits.net/- this one has a dial so I assume that it does not automatically adjust the A/F ratio for you
http://www.eco-flex.us/Default.htm
http://flexfuelus.com/ - not available for Jeep 4.0
Most vehicles built since the late 80's have ethanol compatible fuel systems so my 97 TJ is a worthy candidate. It's also a worthy candidate for building a stroker

My plan so far is:
Crankshaft 3214723 12CW 66lb 4.2L
Connecting Rods stock 6.123" 4.0L
Pistons KB945 +0.060" 11.38cc dish
COMP cam 68-231-4
Head Gasket Mopar/Victor Reinz 0.043"
I will bore out the cylinders 0.060" and mill the deck to 0.
This gives me the following results form the Stroker CR Calculator:
SCR: 11.09
DCR: 9.66
Quench: .043
The above assumes a combustion chamber volume of 56.7cc, not the default 58cc of the calculator. Looking around I have found that 56.7 is more appropriate and inputting a smaller value here increases SCR & DCR so in reality it may be less. I could lower the combustion chamber volume, increasing the compression ratio, by decking the head which might be worth considering.
My goal is to build a high-compression, low end torque-strong motor that doesn't run the risk of burning too lean. I feel that I am on the right track here. I would like anyone to share their experiences with E85 or their opinions of my current path.