I believe the skim doesn't stop it from starting, it will allow it to start for "a moment" and then shut'r down if it fails some skim test. The FSM probably explains this in more detail, I don't have a skim'nabled TJ.
For the no crank, I would double check that your clutch safety is engaging/working/still wired up. That will stop it from cranking and is probably part of that remote start system you took out. I don't even know how those work on a manual, I guess you have to be in neutral? But all that wiring is right in that area, I would look there.
For the no crank, I would double check that your clutch safety is engaging/working/still wired up. That will stop it from cranking and is probably part of that remote start system you took out. I don't even know how those work on a manual, I guess you have to be in neutral? But all that wiring is right in that area, I would look there.