I just soldered all the LEDs on my custom control surface PCB.
Since the PCB and panel were both CNC machined, I was able to do the following:
put the LEDs in the PCB holes
put the panel on top
attach panel to PCB
turn it all over, panel face down on a flat surface
place LEDs in the panel holes
adjust height of the panel/PCB so the LEDs poke through the panel the desired amount (1.5mm)
tack one lead of each LED to hold it
turn it face up and check LEDs are in position
turn it face down again, solder the other leads.
If you’ve designed your panel holes to a grid that matches your PCB, i.e. something like TK’s, 300 mils between LED centers, then it should all work nicely.
If you are using some experimenter boards, aka. veroboard, stripboard, prototyping board, then you might need to bend the leads of the LEDs so they fit diagonally on the board, so the LED center is aligned with a hole, and they’re all aligned with any switches that might also be aligned to the holes. You’ll know what I mean when you start doing it ;D
Anyway, however you go about it, if you solder the LEDs while they’re in the panel holes, that fixes them in alignment, both horizontally and vertically.