Sorry, that I bother you with stupid questions, but I'd like to hear some input from people who knows this stuff, to verify my hypothesis before I'll start fixing not-broken things

My stroker is placed in my friend's 4850 pounds ZJ (heavily modded machine), with HUGE air drag (tire on the roof, 4" lift etc.) but at the time on almost stock tires (235/75R15) makes 0-60 in about 13 seconds. It's too early to dyno it, because it has only 700 miles, but we did this one, short acceleration test, and we were surprised that it took so long. We expected to be somewhere in 11-12 second range. So we are now thinking about possible causes of this behavior.
Specs: 42RE tranny, 0.040" ocerbore, 9.7:1CR, 7.2SCR, Stock 93 Cam (75*AIC), short rods, adjustable FPR, stock 21lbs injectors. Fuel used- 98RON. 5W50 oil.
Now, my thoughts are:
- tranny shifts at 4000- way too early for this engine I suppose. But on the other hand, after turning OD/off it didn't want to rev much above 4000 anyway. Strange with this revver-type timing. AW4 is going to go in, but it has to wait till summer.
- exhaust too restrictive? It is 2.25" diameter exhaust with no cat and only FM44 muffler. To me it looks too tight for this displacement, especially when considering only high-revs power problems. The pipe bent before tranny looks far smaller than 2.25" too. It's the reason I blame most, but my friend didn't have money to make new exhaust now.
- snorkel? It has a snorkel fitted to the box with stock paper filter. Maybe it gives it too much underpressure? The snorkel is necessary in this case, so maybe a K&N filter would help some?
- engine not broken in yet? I know it will loosen up a bit, but I wouldn't expect any huge gains.
- stock throttle body and intake mainfold- these two will be replaced soon (they were planned from the beginning, but we decided to add them later to avoid potential problems), but can it really make that much difference? I expect to gain somewhere between 10 and 20HP from them, so we rather won't break the 12 sec. border.
What I already checked:
- AFR during acceleration stays at the border between rich and optimal on AFR gauge. It may not be the best, but indicates it's not a fuel related problem.
- the o2 sensor is virtually brand new. We installed it 400 miles ago, so AFR should be accurate.
- at startup it spinned the tire (2wd engaged, with truetrac in rear axle, on cold but dry pavement), so it rather doesn't lack power at low revvs. Problem seems to lay at high range of powerband.
-on N it revvs up to 5000 with no problem, which indicates it's not any kind of rev-limiter.
Any input/thoughts/blaming appreciated.

BTW, I must say love this forum, there's so much precious info here

