Regaining frame aligment
A couple things here that could be tripping you up:


Both belt drive and Nuvinci hubs can be noisy all by themselves. Belts frequently also make noise in the stand that vanishes when riding and vice versa. Getting belt tension just right is a whole other step and noise will frequently be the result when it's not dialed. Lubricating it is another piece. (I always use silicone cleaning spray, and yes this is a Gates-sanctioned thing). If the rear cog was visibly out of line with the front, then perhaps this isn't likely to be the problem, but worth mentioning.
When you bent the frame around the second time and the noise went away, it could have affected the belt tension.
If somehow the chainline (beltline) was incorrect with the parts that are on there, it could create the situation where it made noise when the alignment was right and didn't when it was wrong.
Doing what you're attempting without dropout alignment tools or an improvised substitute is iffy. What they do is integral to the whole process of aligning a frame after it's been severely misaligned.


You mention that you're seeing some torsional misalignment between the BB and the front wheel. A way you could go about trying to fix that is taking the fork out, clamping the BB in a vise with some old steel cups, removing the fork and headset, and getting a long steel pipe that mates closely with the inside of the head tube to use as a leverage bar. Then to check the alignment (which you should do first) you can hold the frame up against a light source and eyeball the parallelism between the seatube and headtube. This isn't likely to have any bearing on rear torsional alignment though. You need dropout tools for that. 

Something you can do is take a long, straight piece of square aluminum extrusion, like 80/20, and use it as a straight edge referenced off the bottm bracket. For example, clamping them together in a vise, measuring with a caliper between the seat and the straight edge all the way down their lengths, repeating for the down tube, then removing the straight edge, re-clamping the bb, and reefing on the tubes. If there is shell misalignment, something like this is how you'd fix it.