This is a long complex question with no correct answer.
You need to define your automotive/fabs skills.
What tools you have access too.
What you are building your Jeep for.
Go to this site and start reading the knowledge section to help give you a good idea of whats involved, and what engines you should consider.
Novak Jeep Conversions - Home
I suggest you start reading allot of V8 swap threads here, and on other forums such as Pirate4x4 as well. (search V8 swap)
Popular swaps for TJs include:
5.2/5.9 Chrysler V-8s (90's ZJ/Ram)
Gen III/IV SBC (small block chevys)
Personally I am a big fan of aluminum gen III/IV GM V8s.
P.S. Thank you for your service.