Been working this out for my own 2.9L build. No definitive luck on a bolt together, but some answers between the 2.9l MAF conversion article and talking with the guys at TwEECer. I can post/pm the details if you'd like.
My gut reaction was to turbocharge the 2.9. It's starting to look like I'm better served to go the supercharger route.
The ideal charger looks like the SC14 or the SC12 out of a Toyota Previa or MR2. The SC14 is an absolute testament to badass-ery as its a supercharger rigged to an on-demand electric clutch, complete with bypass valves, etc. for under $500 used. Think Mad Max.
A few folks will absolutely disagree with me on this. I'm good with that. If you'd like, research the build done by
@DCinDC. He has an awesome setup.
Don't completely knock the 2.9 for bigger. Yes, it's a mouse motor. Yes, they have issues from the factory. They also snap to life instantly with the proper setup, have a nearly bulletproof bottom end, and are very easy to source cheap parts for.
The biggest three issues are cracking heads, upper valvetrain oiling, and TFI module detonation. All three are easily fixed. Heads will not crack with the addition of a 4.0l twin row radiator (first gen Explorer/auto/ac/towing - rock auto, $86) and getting rid of the main issue that causes cracked heads, the (and I cannot emphasize this enough) ENGINE DETONATING GARBAGE factory manifolds. If you do put headers on, DO NOT use pacesetter. JBA stainless are cheaper on eBay or the parts section of this forum. Seriously. Ditch the manifolds. They demolished my first set of heads.
Upper valvetrain oiling is solved with aftermarket cam bearings and a new/reversed cam thrust plate. Have a set of rocker arm spacers made. You won't regret it. Run synthetic oil and a Motorcraft filter. Your engine will thank you.
TFI module detonation is easier still. Shielded cable, a used PC heatsink, and a used 12v pc fan.
All of these have been done to mine, with MANY modifications I did not mention. Night and day difference. I will always issue the challenge to any 4.0l fan to knock my 2.9 after driving it (I'll be at the TRS 20th anniversary trail ride). Yes, it doesn't have the "truck grunt" that a 4.0 "sorta" has. It's a European sports saloon engine with oversized intake runners bolted on to change the torque curve. And it's a F***ING BLAST to drive.