I just did the same thing kinda with an old 72 MHz Airtronics 6 ch and an Arduino Pro mini. It is now an 8 channel and the extra channels are programmable and can come from the serial port on the mini :) This lets me use ate ArduinoIMU flat for a head tracker. It uses timers and interrupts for all the PPM I/O. The first time I had it working it was all interrupts and the main loop was empty.
I timed all 6 channels in but only sent out the first four. I discarded ch 5 witch was only a useless 2 pos gear chan. I moved ch 6 to chan 5 and the synthesized 7 thru 8 all on the same timer. Another timer just does the low pulse time. It seems to work perfectly when viewing the input and out put pulses on a 2 chan scope. I just got the concept working and it needs some more testing and code before I would fly with it, but I think it will work just fine.. . I did test it with receiver and servos and the extra channels did my little servo dance :)
How many channels are you able to program?