Yes you can in almost every case– the exception is that you sometimes remove your stock IAT sensor when you remove your MAF/AFM as it’s often built into stock MAF or AFM on many cars. If this is the case, you’ll need to add another IAT sensor to the intake tube, usually just before the throttle body and after the intercooler, if you have one. The idea is to measure the air temp as it enters the engine. After anything heats it up (like a turbo/supercharger) and AFTER anything cools it down (intercooler, meth injection, etc). You want the actual air temp of the air as it enters the engine.
Here’s an article that shows how to measure the resistance curve of your stock (or any really) sensors so that you can input these values into your MegaSquirt EMS via the tuning software for MS2/MS3 ECUs, or via EasyTherm for the MS-I, to calibrate your ECU for your sensors.