NOOO skill saw. Too much power for tiny work. UM, metal cutters might work like what you use on roof flashing or sheet aluminum. Try a hack saw. The problem is that the tub has rounded sides and the grid has straight sides so I was trying to shape at least the bottom one to rest on the ridges that are on the insides of the tub. I did a lot of running back and forth from the tub to the driveway as I didn't want the plastic bits in the grass. Hey, jig saw maybe, or heated knife, or Sawzall. I don't know, something with that much power may be over kill. Also, I wanted the cut edges to not leave a projecting piece of rough plastic. The algae will build up on it badly enough anyway without lots of stringers dangling from it.
Drill a couple of holes in your PVC at the top to let the air out, otherwise it will tend to want to float.
As for the drain, now is the time to put it in the side low near the bottom farthest from the pond. Guess there's no real reason you couldn't put it on the short sides too. We put ours in later.. Worked but a pain to do afterwards. We put a T valve or maybe it was a ball valve--don't remember close to the tub and piped out underground to where there is a retaining wall and out through the wall. Made it easy to catch the sludge in a bucket. But I don't know how peole do it when their Skippy isn't raised enough to do that. To be honest, we cleaned ours with a power washer and shop vac for years and other than being a bit of a pain, it wasn't so bad. But come to think of it, the reason it wasn't so bad was that my DH did it, not me. LOL.