First, I've watched Mark's video and read lots of webpages on alignment, but I still have a question:
I was working on one of my old Seiko's(5139) that I have assembled from three parts watches. I got everything cleaned and the train assembled. I visually looked at the Balance Complete and it looked good. After assembling the train and installing the Balance, it would only swing after I moved it and immediately back to rest. I then looked at the impulse jewel for problems and discovered it was completely missing—not broken but cleanly missing.
I had a balance wheel from another balance 5139 that I swapped to the balance cock and hairspring. I carefully aligned the new wheel with the old wheel before removing for the swap. I marked the new wheel with a Sharpie pen to indicate where the collet should be and the resting place of the impulse jewel. I then installed the new wheel in the exact position as the old wheel. I then adjusted for beat errors and the +- condition. Amplitude was about 252. It looked like I had a good runner.
I assembled the dial and hands and then it was quickly apparent the watch was galloping and running very fast. In a 60 second period it was running 70 seconds. Also, it would stop on occasion as it appeared to bind.
At this point all I can think to do is disassemble the train and visually align the impulse jewel with the pins. Is there another way to align the balance without disassembling the train. It is not a big issue to take it apart, but for future reference I wanted to see if there was a way to align without disassembly. By the way, there is no way to view the jewel and pins—even intense light and high magnification provides no view of the area..
I've seen this on a movement with an incorrect jumper spring where the spring action was too weak to snap the wheel into position.
On the 1664 the different jumper springs have different part numbers (2571 vs. 2583). Likely the springs (and jumpers) are the same as you say but I'd recommend rechecking just to be sure. You shouldn't have to be reshaping a jumper's profile.