Well, I'm glad I didn't give up... things are improving!
I'm still using single-channel transmissions and as far as the deadline goes, that will stay. I did begin streaming data to Excel using Parallax's PLX-DAQ macro which greatly sped up my development pace as I could stream raw numbers to excel and apply calculations there; much quicker than constantly flashing new code, performing a short log and reviewing what is essentially a snap-shot of data.
While I never could get rid of some raw results that strayed far from the area of interest, limiting results to a window and weeding out the ones that fall outside standard deviation produces some fairly nice results, greatly reducing the jitter I've had before. I've also refined the interrupt handling on both ends to reduce (hopefully eliminate) some problems that would cause the transceivers to stop working if the data connection wasn't strong. Now, even in the noisy office, I can stray up to at least 40 feet with no loss of connection, even through a wall and buried in a library of books.
I also took some time to wrap up the hardware and managed to squeeze everything into a 2xAAA battery case... I recommend 2xAA next time. Due to the tight spaces, I ended up wire wrapping the two boards together. All in all it fits into a nice little package and doesn't seem to hurt reception too badly; although code was the biggest problem in that regard.
I've also added a small vibration switch that will ultimately be used to trigger the transponder to send a start message once motion is detected; the aim being to conserve power when at rest. With this case I can manage to fit a 150 mAh battery which provides at least a few hours of battery life; hopefully more once I try to integrate a power saving mode. However, that won't be complete in time for the deadline.