Mine can't be a transmission issue because it's a manual, and it wouldn't "slip" in all gears intermittently, even if it was the clutch it would only slip when it first engages the gear and not once the driveline is engaged. Also, I don't think the OPs issue is a transmission either, I've had two go bad on me and they've never done what he's described. It's a misfire, either a lean misfire from a gummed up or broken injector, or a misfire due to a spark issue.
I've run fuel system cleaner through it on the last two fill ups, and it hasn't helped the issue at all. I data logged it and talked to my tuner, and nothing in the numbers seem to point to anything.
However I did notice some sludge around my thermostat gasket, and now I'm thinking the coil next to it (cylinder 5) might have gotten wet, and could be grounding out. tomorrow I'm going to replace my thermostat and gasket and the boot on the coil and see if that fixes my issue.