1995 Jeep Cherokee OBD scanner

Welcome to the forum. You should be able to get mil codes by cycling the ignition switch. You turn key just till dash lites come on, no further. You cycle key, on--off, on--off, on, then the check engine lite starts flashing, you count the flahes to get the codes. Your looking for two digit codes.

If the donar engine isn't compatible with the computer in the vehicle, It can cause all kinds of problems?

If cranks good but won't start, have a helper crank it, while you visually check for spark at the plugs. If you have spark everywhere, use a gage and check fuel pressure.