I would consider pulling the sub frame and dealing with rust issues before putting the engine in. Based on your pics I suspect the body mount brackets welded on the sub frame under the cowl probably need repair and repairing the floor section where the upper body mount bracket is welded to the floor pan would be easier without the sub frame in place.
Also based on your pics, although a leaking heater core caused a lot of the rust in the front passenger foot well I believe the upper cowl is probably rusted through at the lower corner of the windshield and/or the kick panel vent was leaking. I'd pull that kick panel (being careful not to break off the skinny part) and follow the trail the leak left.
While on a rust hunt before getting too deep I'd look at the rear frame rails and poke them hard with an awl particularly near where the leaf spring pockets are. The other areas like the tail panel, rear window channel, and trunk lip are easier repairs but the rear frame rail/ spring pocket area is a pain without a rotisserie.
With the rust you've got in the floor and what appears to be a T top car you'll need to be careful not to buckle the car as you cut out rusty sections. You may want to weld in supports before getting too much deeper.
I've dealt with all these issues and many more doing restorations, pro touring builds, etc. If you're going to build a car you'll be confident to tour around the province in, you need to start with a solid frame, body mounts, floor pan, etc. While it's more fun to drop in the LQ and drive train you don't want the car to twist up like a pretzel when you're finished.
