Misfire at Idle only (honda)

First off i have a 95 accord LX with the EX motor, you may remember a while ago i posted about my motor drinking water and snapping a rod, but thats why the swap happened. the car ran fine with the stock ECU and stock Distributor after the swap. Now im modding to get it ready for a turbo, i put in the AEM EMS and found that the car would misfire randomly, but i could not figure out why, put the stock ECU back in and it would run fine. I asked the guy im having the car tuned by when the turbo is on it to test the AEM for me as his wife has an accord as well, and it ran fine. So the AEM is ok. so i get ahold of T1 racing and get a hall effect timing setup, to try and fix the random misfire, after some research i found that AEM EMS’ don’t like the stock Honda timing signal. This is a Cam gear and sensor setup, which i cant get working either but thats another problem. Put the cam gear on there and get the timing set again, but in the process ended up dropping the dizzy and chipped off one of the teeth that count the timing to fuel and ignition. put it back to gether the way it was as that is the only dizzy i had at the moment and could not get another from the dealer or NAPA due to funding problems, plus they are like 250 from a store.
got another distributor from someone on eBay, when it came in i took it apart and inspected it to make sure all was well, looked fine to me, put it on the car, noticed that it was the non-vtec dizzy, even though the auction said 95EX distributor, but its ran fine other then the misfire at idle. now if im driving the car, revs above 1500, its smooth as it should be even if i rev all the way out to 6500, no miss, no noticeable loss in power, feels fine. it also surges while at idle, but when i can get it to idle down around 700rpm its a very noticeable misfire. so i don’t think the missing tooth was causing the misfire, altho it did go to limp mode after about 5000rpm, too many timing errors from the missing tooth.
At this point i have the stock ECU in the car, with a wideband O2 that i set up for the AEM EMS that im going to be using when i boost, i had the AEM running just fine, other then the random very slight miss, until the missing tooth problem appeared and i took it out in favor of the OEM ECU as it ran better with the missing tooth. i have not have the chance to up the AEM back in as i do not have access to a laptop on the days that im off from work, mine is dead and the one my father has he is using on those days so im waiting until i can get ahold of that.

now my question to all of you is what else can i look into that might be causing the surge and the miss. i do have 305cc injectors in the car at the moment because the stock injectors that i got with the motor where cracked and i did not want to damage the engine if they failed, so i got ahold of some 305’s for cheap and just tuned the AEM for them to run right. other then that and the wideband O2 its a stock system. I have replaced the plugs, my wires are 6 months old MSD wires, so i don’t think they are bad.

im getting one CEL code for the O2 thats all.

What else should i look at?

Sorry for this being so long i just wanted to give as much info as i could the first time through. Ive been on these forums for quite a while just never ran into a problem that i could not get fixed myself, and i know you guys know what your talking about and i know ill get some good info from you guys.
Thanks in advance.

Edit: some things that i have thought about being the problem or part of it, the O2 no compensating for the richness of the larger injectors might be making the ECU cause the misfire, i dont know if that woudl really happen but it was a thought, mainly because it seems to only happen at idle when the ECU is trying to keep the engine running at a specific RPM. other then that maybe the fact that its a non-vtec dizzy on a vtec motor, but i dont think that would be the case it seems just fine otherwise.

Spark dwell settings or ignition timing at idle in the AEM? If its too long it could misfire at low RPMs from the slow rotation and low battery voltage. How stable is your idle AFR?

hmmmm, its most likely not the distributor, but you could always buy one to try it out and return it once you figure out if that is your problem.

I cant quite figure out whether or not the wrong distributor could cause that problem.

well at the moment im still running on the stock ECU so the AEM is not a problem at the moment, im going to try putting the AEM back in on saterday, but i need a laptop to get the correct config file on there.

the AFR stays pretty solid not alot of fluctuation.

it seems to me that it maybe an electrical problem because its having a hard time starting now too, seems to be worse the colder it is and the longer it sits.

my problem is i dont really have alot of time to try and fix the problem, or the money to be throwing at it on a guess as to what may be wrong, thats why i want to try and narrow it down to what is the best bet to be the problem first so i dont go wasting money on things that are working properly.

any other ideas? does anyone have an extra f22b1 distributor that i could purchase for cheap as a test?