I went with a 4.6L man, there is so much info here, and just by running a google search it's not even funny. I researched this for 3 months before I started anything. Take your time, remember this is your baby, and if your going to spend the money DO IT RIGHT. I'm not saying you need to paint everything and be as anal as I was, just do it right. The biggest peice of advise I can give you LABEL EVERYTHING!! If I didn't label everything I would have been lost. You should have seen my engine bay, it was just TONS of masking tape and notes. Then I have like 30 plastic baggies, labeled, I mean down to the individual bolts. I did diagrams of any unit that had different bolts IE the water pump, I made a diagram, labled it, then labled each bolt with where it fit in the diagram.
My one grip is that I can't get the damn header to seal right, I have a clicky noise which is caused by a leak, which is really pissing me off. While I can't really say that I have tried to address it yet, I'll try to tackle that this weekend.
Also one thing I didn't do is take before pics, and I really wish I had now. Not only for the "This is what it looked like" stuff, but they would have helped in putting it all back together.
Good luck man, and just search 1st, and ask questions here.
BTW, I started here:
http://www.jeep4.0performance.4mg.com/stroker.html and pretty much figured out what I wanted to sink in, and went from there. Anyone good starting point is
http://www.lunghd.com/Tech_Articles/Stroker/Stroker.htm which links a lot of good sites in there, including Dino's site. He is a very active member here, and smarter with engines then I'll ever be
Enjoy!
Todd