I started planning this build before I even bought a jeep. I was in Afghanistan for the better part of a year and needed something to occupy myself with, that being a stroker. I read almost every post I could find on stroker builds, starting from those recipes that have been passed around the net a million times. Combined that with several PMs from several guys that have done some pretty amazing stuff with the I6, and read two solid books on four stroke tuning, and high performance engine design (The books never mentioned the I6 directly, but it was a great way for me to learn the theory behind engine performance, etc).
I am including the above as a quasi disclaimer, so you guys know that I didn't haphazardly whip this motor together.

Some basic info on my build.
Vehicle: 98 Wrangler, 4.0 manual, 112K miles good shape
Everything was fluxed and double checked by the machine shop, real good guys, more on them in my build thread.
Block was out of a 88 Cherokee, had about 200K miles when it was pulled running, for a V8 swap ($50 off ebay) Not alot of block issues in terms of it being so old, bolted right up for the most part
Alabama Cylinder Head, with hescco performance valves and springs, whopping 62.5cc chambers with spark plug (Part of the reason the block got decked), a performance valve job was done, and the valve seats were cut to bring spring pressures down
Comp Cams 68-235-4 Xtreme 4x4™, X4254H, nice overlap lowered my DCR, Comp Cam lifters, stock push rods and rockers
4.2 Crank, Stock 4.0 rods (out of the 88), kb944s
Block decked to zero, quench was .043 with head gasket
I don't have exact numbers for DCR and SCR (Will do a calc again once I do a proper write up) DCR was prolly around 8.8/8.9, SCR mid 9 to high 9s
26lb Accel Fuel injectors, 01 Manifold w/ 4.7 dodge t-body, I cut a six by six square out of it, had a aluminum plate welded in place(which I painstakingly cut the tbody hole out by hand, made a gasket, mounted map sensor directly behind t-body on plate
Gale banks Header, gibson cat back, hesco high flow water pump, stock thermostat
So I finally get the thing started, really high idle, somewhere around 2K, sounds like it was misfiring a little bit, but its happened maybe once every 20 seconds, very light miss, so I continue with initial cam break in. Idle settles around 1400, shut her down changed oil.
Start it up the next day, take it out for a spin, more sluggish than original 4.0, dies on me a few times, bring her home a little disappointed. Started conferring with the fellow gear heads in the family, my gramps is old school and tells me it is the timing and that we need to loosen the distributor and adjust it a few degrees. Show him the FSM and and he backs down. We pull the plugs and re index the dizzy just to be safe. Some of the plugs were way out of spec, one was around .060... (younger brother gapped those for me..... yeah) brought them all back to stock, put them back in. Crossed my fingers and she starts up, no longer missing, still idling high around 2k, no MIL.
Take her out for a gentle spin that night a good hour or two, mixed between highway and side streets. MIL is on now, figure the PCM is just a little freaked by the 4.7. Get some food, start it back up, no MIL still high idle, but is running like a champ, never went over 50% of WOT, but shit, she pulls and purrs like she should. Still got weird looks at the light because the idle is so high but who cares she is running decent.
Long drive to school about 150 miles, varied speed, was pretty gentle (compared to my 90mph dashes back and forth from school I normally do), at one point got stuck in a tight spot between a semi and a large moving van, give it some gas and she is pulling fine, hits 3K and I wouldn't call it a stumble, its like the PCM had a governor on it and cut the motor out for maybe one or two revolutions of the motor (I experienced the same thing in a Dodge Dakota when I tried to take it up 100mph, the governor cuts in around 98

Took it to Autozone to get the codes read, three are pulled: P0113, P0121, P1391.... Bust out my DC Powertrain Diagnostic Procedures for the wrangler
P0113 - Intake air temp sensor voltage too high
Cause: When the IAT sensor goes above 4.9v
Thoughts: I had to extend the wires from wiring harness to get it to reach. I think this is the IAT off of the junkyard intake manifold I bought
P0121 - TP sensor voltage does not agree with MAP sensor
Cause: The PCM performs two tests. When the manifold vacuum is low, the TPS signal should be high. When the manifold vacuum is high, the TPS should be low.
Thoughts: The TPS is an original off of the 4.7 junkyard t-body, maybe at fault? The manual also speaks of the MAP sensor having issues in this section we will see, This code seems to explain poor idle
P1391 - Intermittent loss of Cam pos sensor, or crank pos sensor
Cause: when failure counter reaches 20 for 2 consecutive trips
Thoughts: I feel that this explains the cut out at higher revs. To be honest when we were putting the motor in we had a hell of a time fighting with this thing, I noticed that the Crank sensor was getting smashed into the firewall.... Never thought twice about it because she was running strong that night I took her out, despite the high idle.
Things I am considering at this point.
Tomorrow I am going to test the sensors as best as I can individually as per the FSM, and then going to try and follow the Powertrain manual as best I can sans the DRBIII, I think I can pull off most of the tests with a multimeter and a little ingenuity. If i find failing sensors (FSM tests are pretty straight forward, replace them)
If no luck here swap out TPS with known working one.
Test for vac leaks too.
If that fails going to take her to the dealer, and have those boys square her away.
If that doesn't work, going to try building an adjustable MAP, and pray
Any thoughts or comments would be greatly appreciated. The motor is good, it just some sensor issue. I am posting all of this to help my fellow jeepers out there, so we can debug this together

Thanks in advance.
Mike