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I'd like to be able to queue up some tracks/songs while listening to the radio.

I seem to recall that early early betas did this simply because of omission. It was strange selecting songs from a playlist and then having nothing happen. So (again, if I recall correctly), it was specifically and deliberately changed so that you couldn't work with MP3s when the radio was on. From a user interface standpoint, it's much more logical to do it the way it currently does it. If you could queue MP3s from the radio interface, people would be confused and come in here asking why they didn't play. In other words, "This is by design", so I wouldn't expect to see it changed any time soon.

Why do you even need to do this anyway? How critical is it to listen to radio tunes while selecting MP3 tunes? Why not just listen to MP3 tunes while selecting other MP3 tunes?

However, if you have a computer hooked up via ethernet or serial, you can do this by sending the appropriate commands. The serial and ethernet commands to enqueue tunes work when the radio is on.

Another thing you could do is install two stereos, a CD player and the empeg, having the empeg feed the Aux-in of the CD player. Then you can do whatever you want on the empeg while the other stereo plays.

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Also would like to utilize the time alignment feature in hijack for the radio.

Can't be done as far as I know. The time alignment feature is done to the uncompressed wave audio data bits before being sent to the DSP. The radio signal doesn't get turned into malleable data before going to the audio circuits, there's nowhere it can get its mitts on those bits. So that won't be happening unless you personally implement it in hardware someplace.
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Tony Fabris