Those motor mounts don't look like they were set up for a small block engine. Before you go any further, you need to make some decisions on which way you want to go or you'll be doing everything twice (at least). Don't ask me how I know this......
If it were me, if you have decided to go with a 302 small block, I would get a block to take measurements off of, including your motor mounts. The best ones to get are the Energy Suspension units. I found them at Autozone, but you can get them just about anywhere or on the net.
The existing motor mounts look like they are set up for a big block so you may need to remove them completely and start over again with new pieces. Easiest way is to set the block in place in the frame with it blocked up to the right location and start taking measurements. Most manufacturers mount the engine 1/2" - 3/4" to the passenger side to line everything up with the rear differential pinion.
As far as the tranny mount, it doesn't look like it provides all that much frame rigidity so I doubt you would be losing much by making it a removable unit. You can always replace the missing structure later by installing another 1 or 2 crossmembers across the frame right behind the engine and right behind the tranny to create a bit more stiff frame. It all depends on what you want to do with the car.
What all did you get with the kit you bought? Engine, tranny, etc.....?????
Bob