I'm putting factory air into a 66 442, and I want to eliminate the side vents. On the left side is there a panel that covers the vent hole?

 

The drivers side vent is still there even with the A/C...No panel available that im aware of

 

No panel - you'd have to make one.
The cowl and firewall are different between AC and non-AC cars. Adding factory AC will be a challenge, but not impossible.

 

If you have the donor car and the recipient car side by side, it is an easy transfer. The biggest hassle is cutting the firewall. I suggest that you move all the mechanicals from one engine to the other, and then tackle the evaporator assembly. Once you have it off the donor car, using a large paper bag that you cut so it will lay flat, make a pattern of the opening. Transfer this to the non air car, and make your cut. Better to cut small and then trim as needed, then to cut it oversize. Then start on the dash, and take lots of pictures first. There are many parts that will not be easily recognized once you have them off and try to keep track of what goes where. I would start with the passenger side first, and get everything set on that side, before tackling the drivers side. It is easiest if you remove the glove box liner, radio, steering column, and the front seat. If you don't want to remove the steering column, then at least drop it out of the way. Back in the 1960's I did a bunch of "transplants" on cars that I bought and fixed for resale. When you get everything complete, then double check the right fender inner pan to make sure that it isn't too close to the evaporator / expansion valve piping. This is the only place that I ever seemed to have problems with clearance. It is challenging, but with patience it can be done. I used to figure about 30 hours from start to finish, but many times it took double that time, because you are sitting there looking at the car deciding what to tackle next, or wondering if you needed a band aid to cover the cuts from under the dash.