I know one of the holes in the pic is for the heater fan wiring harness. Anyone have an idea what the other hole might be for?

 

I would hazard a guess and say neither of those holes are "factory". My blower motor has a single wire that comes from a harness behind the fuse box, not through a firewall hole.

 

I'd say the first thing you should do is download the assembly manual.

In Section 0 page 140 it appears hole #1 is the stock 1.18" hole that's drilled during assembly for cars with 1A2C, 35A91, 97C48, or 98C48. Hole #2 I didn't find but I didn't look very hard

My car has hole #1

 

I agree with you Mike, I had looked at Section 0, page 140 in my assembly manual and I came to the same conclusion that hole #1 is for the heater fan wire but I wasn't able to find any reference to hole #2. I initial thought that it was added by a previous owner but sometime back I saw a 69 W31 that had an identical hole in the same location, that’s why I created this post, it may just be coincidental that another car had a similar hole added to it.
One idea did come to me this morning, I wonder if the car had an aftermarket a/c unit added to it, sometime back?