Help! 2005 Mustang Gt Code P2198

[Exile918]

We got through swapping the auto trans to manual on my gt. I went to the dealer to have my keys flashed with my used manual pcm that I found online and just when I thought everything went smoothly the car was running really bad. Cam sensor connector was loose so that got plugged in. After that the car through code P2198 and the mechanic at the dealer told me that the dar was running lean. At that point I had to go to work and if I decided to leave the car at ford it would've meant more money. Drove it home my dad plugged in his obd2 ss annex and it had two codes one was pending and the other P2198. I checked the o2 sensors with a multimeter so it lookes like those are fine. They were fine before we began the swap on the trans so we don't believe that's what the problem is.. I may be wrong tho. The car almost feels like it misfiring the throttle is weird engine is sorta shaky. I looked for a vacuum leak but everything looks in order. If anybody out there can give me some help on where to look I'd appreciate it!!! I hope it's not the used manual pcm I bought online cus I started thinking maybe it's got a tune on it.