Yes you can use the 1.8 tb with the MS. That's what I did back when I had a 1.8t with TEC3 ecu in my 91. Since you have a 1.6 MSPNP you will need to wire in the different tps connector and make a couple of calibration changes so it knows you have variable tps now.

I'm cant remember much about MS programming so I can't tell you exactly what software changes need to be done but the info should be out there, it's been done many times.