@lil_Blue_Ford
Reading your question it sounds like your not certain where you want to go with the engine. I feel that is the first decision and will answer the remaining choices.
Having chosen the power plant, tire size is next based on your engines known max torque RPM and axle gear ratio. The selection of the most efficient tire size is simple math. With your tire diameter dilemma put to bed, it will determine how much lift (or trimming) your chassis will require.
I still like the output, economy and mannerisms of the 2.9l but sourcing OHV 4.0l components, while albeit more expensive, is much simpler. My mechanical mentor is very much in favor of me updating to the SOHC 4.0l platform; my #1 reason to stave that off is the OBD2 system. 5.0 power in a Ranger based platform is arguably the most natural matchup. The horse power to weight ratio is great, only giving up points to overall fuel economy.
I am spoiled with how remarkably flexible the OBD1 PCM remains. Never needing to consider the need to reprogram the PCM has opened my mind to a cost conscious world of fuel economy innovation.
RECOMENDATION
You state that you have a treasure trove of components to work with, just decide how tame or efficient this stock profile that you desire is. I'm a sucker for maximizing fuel economy. No matter where i live, i quickly become faced with undesirable commutes and do not appreciate the ever increasing credit cards exchange at the petroleum depot...if 75% or more of our nation's (world's) automobiles made 35+ mpg, how much different would it be???
In a Bronco II regardless of power plant, here is my immediate short order list:
• Explorer D35/8.8
• 4" suspension lift
• dual James Duff 70/30's on all four corners
Right there is the vehicle Ford should have marketed!! Whether you desire maximum efficiency (fuel economy) from a trusty ole 2.9l, the increased component availability of the more expensive to maintain OHV 4.0l, the improved power and torque of the SOHC 4.0L or a lock and loaded 5.0l set up...is the choice.