It's fairly easy to determine if the vibration is coming from the engine or the transmission. If the vibration occurs when the clutch pedal is pressed in and you have the tranny shifted into any gear while parked, then the engine is the culprit. If the vibration occurs only while the clutch pedal is released so the tranny's input shaft is spinning, then you have a tranny problem.
Swapping a MTX from an N/A into a XR2 would require the flywheel, clutch, axles, clutch pedal assembly, and clutch master cylinder from the N/A donor.
You're better off going to a salvage yard and finding a used XR2 tranny then swapping in the N/A MTX. The N/A MTX is a weaker F series tranny, the clutch is smaller so it won't hold as much power, and the axles aren't equal length which will cause additional torque steer.