I have done several stroker motors, here is what you are looking for.
1. 2000 and newer intake,
2. a crack free exhaust manifold, there are many listed on ebay that replace the stock one.
3. 96 or newer exhaust head pipe, you will recognize it because it goes infront of the oil pan.
4. You can put 5.7 hemi intake and exhaust valves in it for cheap, don't do a chevy valve conversion DAMHIK,
5. an oversize throttle body helps,
6. I use a 258 amc crank, 4.2 rods and then H802CP pistons that were cnc dished to lower the compression down to reasonable levels, offset grind the crank .020 and shave the block so you have a .000 deck height.
7. you want a 7120 casting head, they have the best flow, and with some minor porting and polishing you get a lot of flow improvements
8. and you can look into an adjustable fuel pressure regulator to compensate for the mods you have done....my 94 wrangler stroker acts like a v-8 but needs premium and my wife's 98 TJ is getting 19 mpg without a stroker, just the intake and exhaust manifolds. Tim