I finally made my decisions for a DIY. Spent about a year learning HPTuners with my 4.0 so I could tune it myself. Technically I tried to push the 4.0L and figure out if I could get what I wanted in the stock displacement and determine the answer was no. And during that time I started diving deep into what the different performance options available would offer. I applied bolt on mods to my 4.0L and tuned it about as far as I think I can go. I also knew what I want my Jeep to do and that I wouldn't achieve that with the 4.0L displacement unless I went turbo and that would add complications where I live.
I was originally thinking I would do a 5.0L for the extra bit of low down torque/power the longer 4.060" stroke crank offers. All the bells and whistles, and a much bigger expense than a Golen/Titan/S&J 4.6L. You typically have to clearance the block a bit and always the oil pan for this setup. It's a bit more demanding. Not cheap, but numbers I could easily rationalize vs buying a new car.
I settled on Clegg Stage 2 9.3:1 using the standard 3.895" 4.2L crank. I'll be installing an Edelbrock head unmodified and Cometic 0.027 head gasket which will end up around 9.8:1 static compression. While this head isn't going to win any flow bench numbers, it is a big step up over a stock 0331 TUPY head on intake and exhaust CFM, plus a couple extra tenths of compression, better detonation resistance and more efficient combustion. It should improve power production in the 2000-4000rpm range I care about. This would allow me to leave the block deck height standard and bore standard, while bringing the quench height into a better range to support higher compression. Down the road I'll upgrade to a mild roller cam/roller lifters and refine the power production a bit more. I know I'm leaving something on the table. But it's also simple.
Starting with a good block and head, you could do this for like $1500-$1700 with the thinner gasket. Rough block and more prep work - probably $2500-$2700. Performance cam - add about $600-700. Ported head, LS valves, numbers start adding up quickly. But none of that comes with a warranty someone else handling the break in, etc...