new stroker- no experiance and a few issues

1999 xj - block is from 97 tj stroked to 4.7 with bigger valves, and a big comp cam, everything else is stock. (5000FT above sea level, if it matters)

Alright, so ive got my new stroker up and running, and even got 30 miles on her today. I did not build this motor, so the only info I have is second hand, although I do know it was built by a very good engine shop, and i have some info sheets on the cam. I was told the compression is close to 10:1. I am running fuel with an octane booster (Until it runs out then ill go 91). I have not modified the computer at all. The injectors are stock also, but i was told the engine was designed to run with them. (I have never seen this in any stroker build i have found). The engine does not knock as far as i can tell, but i havent really gone much past half throtle yet.
So here are my problems: one, the check engine light is on, and I believe the code is po340. It says the cam position sensor is not working, but before i did the swap this sensor drove me from CT to CO 2000 miles, and gave me no trouble. I dont want to spend 55$ if i dont have to so let me know what you think. Two, the engine seems to have a little miss, or hesitation on acceleration. Its kind of like when you drive stick, and you dont let the clutch out all the way, then drop it, and it bucks a tiny bit before smoothing out. ( it is a stick, and im not doing that). What might be causing this? Three, im guessing this is associated with problem two, the fact that its still a new engine, and that I am babying it still but although some power is noticable, its nothing huge. Will this change as the rings wear in, and everything seats?
Thanks for your help, this is my first experiance with this kind of swap, and idont know what to expect, so hopefully you all know more.
~John

you need the bigger injectors, I've been researching about strokers a bit to prepare for mine on jeepstrokers.com and from everything I've read you need those and an adjustable MAP sensor. The injectors will account for alot of the power you don't have yet. That's about all I've gathered.

Lack of power & bucking - sounds like fuel delivery or (possibly) ignition timing, but since on a 99 it is all digital I sincerely doubt it is ignition related...
Anyone else?

Def new injectors, if you search ebay for a while you can find some for cheap. I bought a set of 8 Ford24 lb/hr for 55 because one of them was broken or something. An adjustable map sensor will not account for changes throughout the rpm range. Mine has more power than stock but I think i can get more but getting it tuned on a dyno. They might be able to diagnose what the problem is and fix it and give you more power.

I have a theory that the LT1 injectors(24#@43.5psi) are better suited for the obd2 xjs with the 49psi rail(25.5#@49psi) than the FMS injectors(24#@39psi, 27#@49psi). 25.5# is a little rich on my 96, so 27# would be too rich IMO. I'll be data logging mine in the next few weeks to see where it's running rich/lean and give yall the results. Wolfpack likes the lt1s on his obd1 stroker better than the fms, so sometimes even a <24# injector is a good match for a stroker.