Stuck High Idle 3250 RPM

Definitely a vacuum leak. Make sure the intake manifold is aligned and seated properly on the two dowels. It's possible to bolt on the manifold but still not have it seated correctly due to those dowels. Also make sure all of the vacuum lines are connected.

Just for grins, check the throttle position sensor. Mine would idle at 2K, replaced TPS, problem solved. It isn't immediately obvious how the TPS changes idle speed but it's by altering amount of fuel and not telling the computer to take over the idle mixture.
You've had the intake / exhaust manifolds out, the injectors swapped, and the throttle body swapped onto a new manifold. Each and every one of those things *could* result in a vacuum / exhaust leak* leading to high idle by it's lonesome. Buy some brake cleaner (or some water in a spray bottle?) and shoot it at each injector, each port on the intake and at the throttle body in turn. If your idle shoots higher, you've got your leak.
You can also run some Sea Foam in the engine (search for how) through the intake and let the smoke tell you if your exhaust has leaks.
*My thinking is that an exhaust manifold leak could lead to a false lean reading, at which point the computer adds fuel and the idle speed increases. I'm not 100% on that.

As suggested, there is most likely an intake manifold leak or a vacuum leak. You will need to locate and fix that. Start at the intake manifold.

An exhaust leak would not cause high idle.

Solved!!

-New head gasket installation solved High Idle @ 3000RPM

Thankyou,
It was a good call to check the intake and exhaust manifold.
I wrenched checked the manifolds hardware and all were torqued tight.
The intake has 2 notches that hold it in the right spot, those circles where on the notches perfectly in place.
Upon visual inspection everything looked solid.
But even though everything looked good visually,
It was the manifolds. I read to use carburetor fluid while idling, was told the idle would settle and pinpoint a leak.
It worked found manifolds must have leak on a 2 intake ports.
As read and recommended removed and installed the NAPA Felpro gasket
With installation of the head gasket the rpms settled down.
I was able to drive my XJ first time in 7 months.



Currently putting together a build thread. Ill link it if completed.
Has been a lot of projecting and added so much new stuff at once.

Images of my Jeep XJ

Notes:
Make sure to use an rtv copper spray on the gaskets. (Thanks Napa)

I did alot of research and found Bronze was the best bolt hardware for manifolds. (Thanks Fastenal)
Use Loctite 271 or 272 Hi Temp and strength for manifold hardware, Hard to find but worth it. (Thanks Fastenal)