LSJ - Help with idle misfires.

I installed a stage 2 kit last month on my Ion Redline, with a 2.9" pulley and 60lb injectors, and started with a base tune emailed from the shop. I've dialed in the MAF fairly well, but it's misfiring at idle in one cylinder (and sometimes while cruising).
The misfire counter will usually increase up to around 14 or so, then reset to 0 and count up again, repeating until I start moving again. I have seen it count as high as 80 to 100 on occasion.

I swapped plugs and coil packs around, but the misfire stayed on cylinder 1. After swapping the injectors between cyl1 and cyl2, the misfires moved to cyl2, so I figure it could possibly be a problem with the injector. However, when I set the MAF fail to 0Hz to tune the VE table the misfires completely went away. I'll try cleaning my MAF tomorrow, but since the misfires moved with the injector I'm not sure a dirty MAF would be the cause.

Has anyone had an issue like this, or any ideas on how to fix it?
Here's the files for the MAF enabled and VE only tunes; and the scans showing the misfires on cyl1 and cyl2 with the MAF enabled, and with no misfires with the MAF disabled.