I have the same problem with the side panel being slightly warped, though it doesn't affect usage for me. It was a common issue on the P180's too. They are 3-layer panels for soundproofing, and if one layer gets misaligned or warped due to heat or other means, it can be a pain. Replacements are available from Antec, you can get in touch with them via the website if you need to.
No need to mount a fan in front of the HDD cage. The middle is enough, only problem is it can make PSU and HDD cables a pain to route. This design was changed in the P183, which now indeed has the fan at the front. Cooling with the middle fan is fine though, my HDD temps are good.
I have the same PSU in my case and it's mounted with the fan down. That way, less dust gets in and there's no danger of dropping screws in etc. There is enough clearance below for it to have plenty of cool air. There is a brace/bracket to mount it in if you wish too. It is a bit tight, but dampens the vibrations, not that the HX620 is loud.