Im about to fit a Magnaflow system over the holiday season.

Does anyone remove the exhaust heatshield to make more space?

Opinions????

I removed mine but I have a Magnaflow bullet style muffler under the rear seat, so not as much heat under my gas tank as there might be with a crossflow style muffler.

I was thinking of the one where the exhaust goes over the axle as well?

Yeah. All mine are gone. Just pipe back there now. You can see where the muffler is just above the letter E.

I would leave them as you shouldn't have any issues with clearance. I have a 3.5" exhaust and dont' have any issues.