Yeah, I use hot glue. Works most of the time, just watch out about gluing exposed solder to a conductive surface.

Sometimes if I'm feeling fancy I'll 3d print a custom little mounting bracket.

Cutting out holes, if you want them to be straight I recommend getting a little press stand for a dremel, like this. Or a drill press if you think you'll use it a lot. Or just get really good at holding your hands perfectly perpendicular and steady.

Make sure you measure and mark your hole centers, it looks more visually pleasing if you space them out evenly and take into account how far away they need to be from edges and other controls.

Cutting out square holes, that can be a real headache. If you're just limited to hand tools, I would use a drill or reamer to make a hole, then use a small file to widen the holes and make corners by sawing/sanding away at it.

I stopped doing that kinda stuff by hand because I got tired of dealing with it, now I use a CNC machine and design it on my computer, then it just does everything perfectly as I designed it. Makes it easy to do a completely custom enclosure and also lets you label the controls in the material.