I got the driver's side on fine, but on the passenger side when I compress the piston with a c clamp and old pad I can't get the boot in right; it keeps puffing out. I've never actually had this be an issue before. Any suggestions?

 

Got a picture?

Generally, as long as the rubber piston boot doesn't get pinched it won't be a problem. On some Toyotas, they puff out like nothing you normally see on a Honda.

 

If the boot isn't fitting there is rust or something you missed in that grove, take it apart and get a small straight screwdriver and run it around the grove to feel if there is a rust bump you missed.

Scrape that grove as good as you can, then the boot will fit, I have had that problem hundreds of times.