You've got too adjust the OLMA tables yourself to what you think is acceptable for the gas your running (samething with timing, OLMT). Estimated AFRs should match logged afrs if everything is lined up 100%. Its not the easiest thing in the world to do, but it can be done. The 3 main things that have to be on point for your Estimated AFRS to match your logged AFRS are injector global settings, airflow (if your running a maf) and zero boost leaks, if any of these 3 are incorrect/present your logged afrs will not match your estimated AFRs, of course theres other variables as well (fuel pressure) etc.
As for the misfire your experiencing- I would throw in a set of brand new NGK BPR7ES and gap them around .020-.022, and go from there. Theres two ways you can safely lean the tune out some, you can do it either by going to the ECU_config -> Fuel Tab...once your here you can goto any RPM you like and add or subtrack the amount of fuel youd like (with the car running). The other way to do this (the correct but harder way) is adjust the OLMA table by logging loadfactor (which I believe is done stock when running ECMlink). Loadfactor will tell you exacly which load cell your at, then you simply adjust that load cell to whatever AFR you think is acceptable. The ECU will now try to target that new AFR you entered into the load-cell then your basically finished (The same exact method is done for the OLMT maps also). Its not guaranteed to match the AFR you entered like I said above b/c of other reasons but if your comfortable give it a shot. The only downside is the Direct Access-OLMA method usually takes longer per say then adjusting fuel sliders up/down, and can only be done with the car off. I spoke with Tom and Dave (the creators of ECMlink) a while ago and they're was trying to make the DA tables adjustable with the car still running but this hasnt been finished yet.