This perhaps is a dumb question and I assume I can but just to be sure. Can I attach a crystal oscillator to my arduino pin and then to the infrared led instead of using registers? Yes or No?
Still not clear on exactly what you are trying to do. If you drive the IR LED directly with a crystal oscillator (38 kHz or anything else) there's no data there, just a steady carrier. So maybe you are trying to modulate that carrier with the Arduino? It sounds like your plan is to use an output pin to power the crystal oscillator, and modulate by essentially turning the power off and on. This is probably not such a good idea. Even if the Arduino pin could handle the current (doubtful), the crystal oscillator might not take kindly to this approach... it's meant to go on and stay on.
So you need some sort of switching circuit. Depending on what you have on hand, you could connect the Arduino (modulator) output through a resistor to the base of an NPN transistor. The emitter of the transistor goes to the high side of the LED and the collector goes through the LED's dropping resistor to the +5 rail. If this is a low-power LED then you may be able to use the +5 from the Arduino itself, and a small-signal transistor. If you have a powerful LED, you'll not only need a separate supply, but a power transistor as well... and maybe wired with a small signal driver in a Darlington configuration if the power transistor needs more base current than the Arduino can give. Lots of other switching options, but we need to know more details! Boggyman