As it turns out, back in November I bought the Sony STR-DA80ES Receiver (half price since its last year's model). Although the new 50ES was available, I resisted the temptation of its remote largely due to this web site (and in hind sight, one of my better decisions).
I have managed to input all of the functions except for some of the "internal" macros found on the Sony remote.

For example, (using the Sony remote), I press "TV" and the Receiver switches to "TV" and the TV (Sony XBR(2)96-32") turns on as well. The same applies when I press "Video 1" (for the VCR); the Receiver switches to "Video 1", the TV turns on and goes directly to Video 1 on the TV.

Unfortunately, despite a number of attempts, I can't get the Pronto to learn these "multi-function" inputs without creating a seperate macro via the Pronto. What's great about the Sony remote is that no matter where I leave the "Video" position setting on the TV (4 in total), it will always return to "Video 1" after only one sustained press. The same applies to the TV button, but not for "Video 2" or "Video 3".

I think some people here have overcome this problem and have managed to get the Pronto to learn these multi-codes without resorting to Pronto's macros. Any suggestions or do I have to wait for the software?

Otherwise, I'm very pleased with both the Pronto and the Sony STR-DA80ES and they seem to get along just fine.