I'll just CA the engine on while i am building, and then remove the mounts and drill the holes on the drill press at work once i have the wing on, and some idea of balance.
You really don't need the engine on the mounts for anything until it's time to mount the cowl. It's heavy and makes handling the fuse somewhat more of a problem. When you need to drill for the motor control rod, simply hold the engine in place and eyeball the location. Works good for me. I've always liked to keep the engine away from all the dust and glue drips etc....
Also, when drilling the holes in the mounts, do i just use an everyday punch that you use in metal work to make a little dint, then drill the holes on the drill press? I have never worked with 'glass filled' mounts before!
A punch works. I've found that it can be offcenter. Any marking tool that has some bulk will be hard to hold square. The engine gets in the way more on one side than the other. I've used pencil leads and have a very slim pencil I use now. It's easy to mark the entire area of the mount down in the holes in the engine flanges. And the drill press accuracy is up to you anyway. BTW, it's really good to use a press vice to hold the work. I'm betting you already do.
As for needle valve placement, I assume I just make sure it protrudes somewhere outside the balsa cowl for adjustments - it doesn't matter if it is horizontal or vertical?
It makes not one whit of a difference. And the needle body on that engine can be fitted a couple of directions with no problems. It can also be moved off the engine, but it's not worth the effort.