You've had some stuff going on with your car lately, hey Ryan.
I also don't think it's the cruise as mine hasn't given me that problem either (although I don't drive it much ), but like you say - it's easy to rule out as it only takes a minute to unplug the throttle harness.
If the fault appears semi-regularly now, it shouldn't be long before you know. Hopefully it's not the F-Con but a TPS as that's means the F-Con is OK (as the last 'electrical' mod you've done it has to be high on the list of possibilities). It could also be the cruise control interacting badly with the F-Con, but I don't know anything about how they wire in so just throwing it out there...
The timing of the fault is a bit of a coincidence with the F-Con going in though, & I have a hard time believing coincidences, so good luck with the fault finding.