Dino unless for some reason you have a manifold that has poor casting don't bother with the gasket match... You want to port match, the gasket is irrelevant (and if its the MLS gasket it is pretty damn close to matching the port already).
I sim'ed the 99+ intake in Engine Analyzer Pro in a thread over in performance and it came out at about 3hp peake and 10 foot pounds through much of the RPM range, which pretty much matches what both you and Lee Hurley have said about it. The primary benefit besides the benefit of more equal flow, is the extra 4 inches of runner length. This tunes the torque peak for considerably more mid range torque than the shorter square intakes. It also LOSSES horse power... In fact if the 99+ wasn't so smoothly designed it would have LESS hp than earlier intakes, only because the torque curve is moved lower in the RPM range. However because it is a much better intake it still manages to gain a few hp. It's design intent is clearly to increase torque which it does a great job of.
If you want a nice boost in HP cut a couple inches out of it and TIG weld it back together... this moves torque higher in the RPM range. up to a point it will even boost the peak torque number a few more foot lbs.
Comanch91's results are also on a stroker, the stroker may put more demands on the intake especially if its got a non stock cam grind. I agree on the mallcrawlin thread... that guys 4.0 was hurting on the baseline runs... so his results are inflated.
Incidentally your mustang TB mod looks like it was worth around 4hp nice bang for the buck but I think a $50 dollar 99+ intake is even better.
I wouldn't speculate at factory changes and try to compare them to factory net power ratings, that's futile

those ratings aren't accurate enough to throw 3hp changes around... The 0331 head probably makes better power than any other casting. Those iron exhaust manifolds probably add mid range torque with a loss of peak horse power over the previous factory tube headers. They are way better matched to the exhaust port than the factory tubes are. The only physical thing that hurts the 2000+ 4.0 is the pre cats, and they hurt a lot... those pre cats are right in prime scavenging pulse territory for a 4.0L engine. They hurt scavenging but that's where the factory had to put them to meet requirements. You don't have to look any further than the pre cats to find what Jeep was trying to overcome to make more torque. IMHO anyway.
And once again Comanche91 that is the cleanest engine bay I've ever seen in an MJ...