Ok, here is some more details and updated test results.
The transmitters are running at 300Mhz. The data stream is a 25%/75%, such that a "zero" is 25 high, 75 % low, while a "one" is 75/25. The bit period is 1.97ms. Basically, it works just like any older (non-rolling key) garage door opener. During testing, no transmitters are active and the antenna is removed. The rf section is running off a 8v linear regulator and the micro has a 5v linear. The rf and micro grounds are only common at one point.
The "noise" that I see, is at pin 13 (input of rf, PA0) the voltage is at or near zero volts. There is the occasional quick noise spike (inherant with super-regen), but the pulse widths are very small. The "sleep mode" noise that I see is a signal that goes from near zero to 5 volts and stays high for ~24ms, and then drops low again. This, of course lines up perfectly with my 6ms task * 4 loops. The next time the micor wakes up (160ms later) the same waveform can be seen. I just checked the code and PA0 (input capture input) does not have the internal pull up resistor enabled.
What is interesting is that I removed both regulators and fed in two separate power supplies. With just the power and ground pins connected, no noise. If I then connect pin 13, the noise comes back.
I am pulling my hair out! To further complicate matters, if I disable the s/w which enters sleep mode, I don't see any micro based noise. This makes me believe that it is related to the rapid change in current. I tried a choke in the power line, but since each section has its own regulator, it didn't seem to do anything.
Thanks for all the help and support.
Joe