How to align components for front panels
From your somewhat scrambled description you only have problems with LEDs... which is strange because the LEDs are the only components with long flexible leads that could be bent easily to required position.

So, bend the leads to get the LEDs as close to required position as possible but do not solder them. With everything else in place attach your perfboard to front panel, guiding LEDs into their holes. Then solder them, while holding steady in required position.

If you are OK with LEDs sticking out a bit, push them forward until the flange is flush with back of the front panel before soldering. This will ensure perfect alignment of them all.