Thanks for the help both Darrel and Bruce!

I kicked myself for not seeing that I wasn't resetting the Counts in my first posting However, things are working well now, and I can read my IR signal as I want by putting the clock routine as my interrupt and the IR PULSIN command as my main (as Darrel suggested). At this point is it just some coding to recognize alarms and different programmable options that I will throw in.

I don't think I will have a problem with having enough time for tasks between interrupts since I am only doing the initial PULSIN command in my Main. If there was some kind of restriction in the interrupt routine I might have a problem them, but most of the heavy coding will be outside the main and the Interrupt routine. Though the code Bruce posted is very concise. I will try things out with both of them and see how things go.

Ill post here if I have any more questions.