I just replaced all the front suspension bushings including the upper and lower bumper stops, I also have Hotkiss 2" lowered front end and the lower bumper is within a couple of inches of bottoming out. Has anyone had to cut the hump off the lower bumped stop with lowered suspension?

I haven't had any issues.

Is the car on the ground at ride height? As soon as you put weight the suspension, your control arms will adjust, clearing the control arm bumpers. I hope I understood your question correctly.

A couple of inches at the bump stop will give you almost twice that at the wheel. Shouldn't be a problem.

I haven't had any issues with mine and my car seems to sit lower than allot I've seen.