Hotwire PCM questions

Very interested to see how this one pan's out on this Riddler. I have a 07' 5.7 hemi which I bolted the challenger 6spd to. I'm using a 05 ram computer that was flashed by Hotwire which I stated would run a manual transmission.

The car runs, having some issues so it may not be transmission related and could be something else, but I do notice when I pull up to a stop or to a low speed with the clutch fully in that the engine will feel and sound like it is about to cut out, then the revs pick up again, idle drops right down, revs pick up. It does this a few times before regathering it's idle to normal. Meanwhile you can see this causes the oil pressure to drop, return, drop, return to normal. I'm wondering if this is the issue they are referring to?

It's really starting to get to me.