Radiator underneath was smaller as was an intake on the port cowling. There is also a difference in the main gear doors but I haven't found any clear shots yet.
As far as the main gear doors are concerned... you are right. The MiG-1 had them ,let's say, in one piece. The main part of it coverning directly the wheel, consisted of two parts being folded with a hinge at the 90 degrees along a straight line. The MiG-3 had it as two separate parts, the main one attached to the gear leg and the second one to the fuselage. The bottom edge of the main door part wasn't a straight line. Here pictures. In the enlarged part of the picture of the captured MiG the MiG-1 door type can be seen. Because the pic of MiG-1, I've clipped the early doors, shows the side air intake (under the exhaust pipes) of shape almost the same of the MiG-3 we can say the captured plane was MiG-1.