Off the top of my head...remember the old XModem and Zmodem? Those might come in handy...
If I was you, I'd use RTP...Ron's Transfer Protocol. I've used something similar in the past, JTP...Jeremy's Transfer Protocol!

Seriously though...if the RF transfer works at close to 100%, then just go with whatever you think works. I built an MP3 player that uses a USB port (FTDI based). I use 513 byte blocks. I send out a load of $ff for sync'ing, at least a block worth, over 512 of them, send a block ID ($01=file length+file name, $03=file data, etc.etc), then send off the data, maybe three times in your case, best 2 out of 3 wins the block in case you get one or two corrupt bytes, then an end of block sequence, another dozen $ff's, then restart at the block ID mark...

Or whatever works...not much help I know. But if you're that confident in your RF method, you should need much error checking or identification. You're receiver firmware should know and expect what's coming next.

JDG