It's not critical in the sense that you ruined the tuner's ability to tune stations properly or process the signal -- you did not do that, and you cannot do that with the separation control. The controls that do those things are tuning coils and transformers that need a stereo fm signal generator and an oscilloscope to adjust them correctly. There are a whole series of coils, and changing one affects all the other ones, so they must be done in a particular order using the correct test equipment. They are also completely inside the unit, not sitting on top.
The separation control is not an adjustable coil, but a variable resistor (pot) that helps achieve the best channel separation. It is generally the last control to be adjusted in the realignment process, and adjusting it will not affect the previous tuning/alignment work. If you can input a signal with a song that you know has complete channel separation (ie, the mentioned Beatles song where the vocals are on one channel and the instruments on the other), then you can turn the balance control all the way in one direction, and adjust the separation control so that you can't hear (or hear a minimum of) any of the stuff that is supposed to be on the other channel.
If the separation control is on a preamp circuit, and not just on the FM circuit, you may be able to use the phono or aux input for the music signal. Otherwise you need to input the signal into the antenna jack, but you may need to use a matching pad to get the impedance right. You could potentially use an iPod in the antenna jack, but it would need to be turned down very very low to keep from overloading the circuit. Not sure it could go that low actually. FM signals are in the microvolt level. Phono inputs are in the millivolt level, whereas line-level aux signals may be around 1 volt. The FM transmitter suggested would be best, if you have one. It would be the right level.
Or you could just adjust it so it sounds best to your ears. And don't worry about it. You haven't broken anything.
