tl1r, I'm one of the first dozen or so people to build a stroker, built mine back in 98 BEFORE there was a "strokers" group (
http://autos.groups.yahoo.com/group/strokers/ -- you may want to drop over there!).
I'm just going to go over a couple things that have mostly been mentioned.
1. Indexing the distributor is the same for all 4.0L engines. All it does is adjust the position of the cam position sensor and tip of the rotor to the cap towers. The rotor has a wide tip so when the computer tells the ignition to fire the tip will be in conatact with the proper tower. Move it to far off and you "lose fire" to early or have a short fire because the tip wasn't in position yet. Has nothing to do with timing. The only reason you have to index the distributor is because aftermarket cams (and even some factory replacements) don't have the drive gear in the exact same place on every cam. Same for the distro drive gear. The position of the gears can be off from the factory installed parts, so the distributor needs repositioning.
2. Sounds like you have a CPS relocating kit. You CAN change the timing by moving the CPS. Even if you have one in the stock location you can move it a little. Just pull the CPS then slot the holes. Moving it about 1/8" clockwise or coutner clockwise will change the timing a few degrees. If you need more than that you need some more engine work.
3. The Renix system is a bit more tolerant of compression changes, but will still ping on 87 if stock components are used to build a stroker. That's how I built mine -- stock 4.0L pistons, 258 crank and rods, NAPA "Econo-Power" 258 cam. It would ping under load with 87, only under heavy load with 89. I later machined the dish in the piston deeper to bring compression down to 9:1, and it doesn't ping on 87. I'm not sure if an HO engine would or not, but the knock sensor doesn't have the range to tune out ping at 9.5:1.
4. You can use a cam with a lot of overlap to bleed pressure. If building a "budget stroker" that's the easy way to do it. You "lose" 10 hp (+/- 2-3), but that extra 10 ponies will cost you $600 or so in custom pistons. You will still get a 50 hp increase even with the high overlap cam, and the only cost over a stock rebuild is for a used 258 crank and rods. I don't count machine work to those, you'd need the work on an old 4.0L crank and rods too.
5. To get the highest power you need to worry about quench and maybe use the 4.0L rods, but that will cost $2000 or so more than a build with stock components. You'll only get 15 or so extra ponies (5 more than custom pistons) for the extra dough. For a budget 250 hp engine, worry more about compression and forget quench height. Only when running over 9:1 compression does quench make any difference in the 4.0L.
6. The HO computer system is a little harder to fool. This is mainly due to the timing program modifications required to eliminate the knock sensor and EGR valve.
7. Looks like you hit on the main thing used to fine tune the engine -- the adjustable MAP sensor! Yes, it's only needed to correct tuning. But the tuning requirements changes when the engine was modified and the computer kept stock. The only other thing to do is use an aftermarket programmable computer such as the MegaSquirt or SDS (
www.sdsefi.com).
Glad to see you have it under control! There's a bit of a learning curve to building strokers, as you found out! The strokers group will help as well as this link:
http://www.jeep4.0performance.4mg.com/stroker.html.