Does putting panels all the way around the AD5M cause heat issues for the mainboard?

Warm but not hot to the touch near the board is normal, especially on a longer PLA run. The AD5M's board and PSU are passively cooled mostly by the air moving thru the open frame, so once you close the walls they'll run a few degrees warmer than before. What you want to watch for is the power supply getting too hot to keep your fingers on for more than a couple seconds, or the board area smelling like hot electronics. Neither of those happening means you're probaly fine for PLA. ABS is a diferent story though, because you'll be heating the chamber deliberately on top of whatever the electronics generate.

Before you cut anything, run the printer with the enclosure fully closed and doors sealed for an hour or two at room temp with no heated chamber, then feel around the PSU and board again. That gives you a baseline. If it's just warm, you don't need a big vent, maybe just a couple of passive vent holes low on one side panel and high on the other so air can drift through. Keep them away from the bed level so you don't dump your chamber heat when you do start ABS, since the whole point of the enclosure is holding warmth around the print.

For the chamber fan question, I ran into the same gantry clearance issue on mine. The spot that works is mounting a small fan blowing across the top rear of the chamber, up near where the top panel meets the back wall, angled down slightly. The gantry rarely gets that high at the rear corners. Keep the fan below the top rail and offset to one side and it clears the toolhead on full travel. Use a slow fan, not a blaster, because anything moving fast will cool the chamber and also mess with surface finish on ABS from part cooling drafts.

One more thing since you're printing panels: leave the PSU side panel removable with thumb screws or magnets if you can. When you eventually need to rewire or replace something, you'll thank yourself.

Agree on the removable PSU panel, that advice saved me on mine. I did mine with magnets and a couple of knurled screws at the corners, and I've allready had to pull it twice, once for a cable that worked loose and once just to blow dust out of the supply. Takes ten seconds now instead of undoing a whole panel. Only thing I'd add is check the magnet strength, weak ones let the panel rattle against the frame on faster prints and it drove me nuts till I swapped them for bigger ones.

On the vent holes, one thing that helped me was cutting them oversize and covering the inside with the adhesive foam weatherstrip stuff you use on drafty house doors. I folded a square of it into a baffle so air still moves through but light and drafts are blocked. That way I could open the vents up for long PLA runs and mostly close them off with a flap when I switch to ABS, no redrilling later. Also grab a cheap IR thermometer gun if you have one around. Pointing it at the PSU case every half hour during a test run tells you way more than poking at it with a finger, and you can watch the trend instead of guessing.