2.9l and 4.0l OHV('90-'00) use the same block, so motor mounts and transmission bell housings match up.
2.9l = 140 horse power
4.0l OHV = 160HP
But the swap to 4.0l would also require full engine wiring swap with some parts(MAF sensor setup) and 4.0l computer.
Any other engine swap would require the same but also another transmission to match new block.
Good info here, on the 2.9l and swapping engines:
http://www.therangerstation.com/tech_library/index-engine-fuel.shtml
You can just rebuild the 2.9l but not up grade it's internals for more HP
Your current computer setup uses Speed Density software to calculate air/fuel mix, this is programmed for the stock 2.9l engine, what this means is that if you were to add a bigger Cam or turbo the software wouldn't be able to add more fuel because it can't "see" the higher air flow into the engine, so the upgrades wouldn't change power by much.
You can of course change computer software, although that is not inexpensive.
Ford switched to MAF(mass air flow) sensor and software in the early '90s on some engines, this allowed you to increase air flow and get more fuel in each cylinder so more power to the wheels.
ebay often has good deals on rebuild kits
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