What you describe is a common problem when fitting big diameter pipes to the 1200's. I cant actually remember what a standard engine mount looks like
Your ideas do sound OK and obviously you are aware of the strength issues associated with engine mounts in a rally car, they do cop a pounding and your suggestions sound OK as long as you keep in mind the strength issues.
My engine/pipe set up has the same problems with the pipes interfering with the mounts so new mounts have been fabricated with cut outs in them for the pipe then they are reinforced. Every bit of metal that can be retained has been retained. There is about 2mm clearance around the pipe,I even have to jack the motor up to allow enough clearance to remove the pipes.
My car won the NSW championship in 2000 and has been rallied hard since and I still havent had to replace the engine mounts.
It's very difficult for me to give engineering advice over the web all I can suggest is that you just keep things as strong as you can and as with any new mods, keep checking them in service.

Good luck.