Whoa dude sounds like you got a whole bunch of problems there. Is it the '05 or the '12 bike?
2012 Roadster.
I'd download the PCV install instructions and check the installation is legit. E.g. your crank sensor plug not being connected meant the PCV don't know what RPM the engine is at and hence can't accurately fuel.
Then plug it into computer and update the firmware on the PCV (mine went bonkers a few years ago, ran real lean etc like yours, and a firmware update fixed it).
I'd also hookup TuneBoy / TuneECU for the diagnostics and see what your MAP vacuum readings are like.
Yes to updating the firmware and checking all the connections. Checked the ECU, and no codes stored and MAP reading looked fine at idle and slight throttle.
Here is a 9000rpm Rocket PCV map template;
9000rpm Rocket III PCV Map Template (Superfine % Throttle)
Re Tuneboy; did you get a copy of your Tuneboy map from Carpenter in an email?
No. Was told I needed the ECU Serial number, which I now have. That is how I found out the VIN numbers were different.
I've a suspicion that Tuneboy maps (9000rpm ones at least) can only be read by certain versions of the TuneEdit (Tuneboy map editor) program.
So you'd need to get that TuneEdit version off Carpenter too to read the map.
Regardless, if you wish to go TuneECU with the map;
04-09 Standard/Classic
Carpenter Racing 240hp map (TuneECU version) - older Rockets
10-present Roadster
Carpenter Racing 240hp map (TuneECU version)