The installation guide is only showing wiring for automatic transmission. Did you wire in the clutch bypass ?
The clutch signal is a yellow/dark blue wire at the clutch switch. Negative trigger. You can use the small white wire in the 20-pin connector for that.
Second, manual transsmission vehicle require that you do Ready Mode in order to be able to remote start. Ready mode is what tells the unit, car is in neutral. https://fortin.ca/en/download/87611/87611.pdf
Enable option 33.2 since you are using the oem remote and follow option 3 in the guide above. Since you have a turbo timer enabled, vehicle would run 4 minutes and not shutdown on door close like mentionned.