The work you are doing is valuable experience.
You have already figured out that it is better to route the truss rod channel when the neck blank is square rather than after bandsawing it to its rough taper.
When gluing a fretboard to a neck, its helpful to insert some small pins into the neck and align the fretboard on the pins before gluing. Once you have the glue spread, you can then fit the fretboard back onto the pins so when you clamp it down it doesn't move.
I agree with Devon that you can line up the centerline of the neck to the centerline of the body. That works if you have routed the neck pocket on the centerline. I suggest you always use the centerline of the body as a reference for neck pocket, pickup routes, etc.
Once you have that fitted, you can see if the fret slots are perpendicular to the line where your bridge will be i.e. the distance from the bridge to the nut should be the same on either side of the neck (i.e. both e strings). You could also measure the distance from the bridge line to the 12th fret for example and see if the two distances are the same. It may be possible to adjust for slight imperfections by adjusting the intonation, but I'm not sure how much leeway you have.
You say you routed the fretboard flush after gluing it on the neck but it came out wavy. Did you use a neck template to guide the router of route by hand? If a template, you shouldn't have a wavy result. If not, you are lucky waves are the only problem. I once again agree with Devon that a long flat sanding block is useful.
I suggest buying Melvyn Hiscock's excellent book on guitar making. All these questions are addressed there.
Good luck.