You Pay Your Money And You Take Your Chances
A fuel injected 2.9 would have a more power than a carbed 2.8, and possibly better gas mileage.
The BIG issue, to me, is reliability. It's a real crapshoot with the 2.9. If you've been reading the posts for a while, you'll notice two common problems with 2.9 engines.
First, cracked heads. The original cylinder heads were prone to cracking if you ran a little too hot. Depending on where the crack occurs, it can lead to a destroyed engine (antifreeze in oil...very bad). This can be avoided by buying aftermarket heads.
Second, lifter noise. In this engine, it's a symptom of a serious oil pressure problem caused by a bad camshaft bearing. Oil pressure is fed through an anular groove cut into one of the camshaft bearings, and passes up through passages to the lifter galleys and rocker shafts. This works OK as long as that camshaft bearing doesn't get sloppy. For some strange reason, it does. The oil pisses out from between the camshaft bearing and cam journal, and your valve train doesn't get enough oil pressure to work properly. In some cases, this could cause low oil pressure at idle speed. Ford recognized this problem, and quietly changed the circuit for the electric oil pressure gauge to cover it up (unless the pressure got VERY low, which is how I found it). Replacing the cam bearings, using synthetic oil, and changing oil & filter religiously would probably fix the problem. I have 84,000 on my remanufactured engine. I'll let you know in about another 40,000 miles.
When working properly, the 2.9 is a relatively good engine. Peppy for its size. Personally, I like it. But if I had to do it again, I'd go for the 4.0.
Look, you're going to do a lot of work to put in a 2.9 or a 4.0. Sell your donor vehicle, save up some money, and buy a beat up explorer with a 4.0. I think you'd have most of what you need there. Others here can tell you more about that.
That 2.9 may look attractive because you got it already. But believe me, you may very well end up spending a lot more bucks and ending up with more headaches than what you got now.
Get the 4.0. Check out the horsepower and torque difference!