Hi Jason, sounds like you're learning, which is what a first model is all about, so while you want to do meticulous, detailed preparation, don't sweat the minor imperfections. All of us have learned the tricks as we go. Each model you build will turn out better than the last, you'll find your own favorite methods of doing all this stuff. For instance, you'll learn to glue some 1/16 plywood scrap to hardwood servo rails to prevent splitting. Each covering job you do will go better than the last. etc. etc.

A standard drill index from a hardware store will do all you need. They start at 1/16-inch and go up in 1/64 intervals, then 1/32 intervals above 3/16 or so.

You'll also learn that vibration can and will loosen everything! Loctite is a great way to prevent losing parts in the air, we've all seen engines fall off 100 feet up, dangling by the throttle cable! These practices seem redundant because they are. Redundancy is a great airplane saver.

For mounting a .46 to a nylon engine mount, I like to use 6-32 cap screws and nylock nuts. The cap screw are hardened and won't break off later. They're also often easier to access in the finished model, as they accept an Allen wrench. Yes, thread the engine mount, and use a long enough bolt to pass through, then add the locknut on the bottom...with Loctite
I've also flown plenty of .46's with the cap screw simply Loctited into the threaded nylon, never a problem.

best wishes!