Welcome! I think your plan is fine. I only had a 1 DIN slot in my van so the options of another head unit was out, but I would have replaced the factory system eventually anyway (it really sucked).
A couple of comments (it's what you asked for):
1)
I plan on feeding the empeg into the HU, so I can use the HU's wheel-mounted remote for as much as possible.
I may be unclear as to what you mean by this, but it doesn't matter how the empeg is connected when it comes to using the remote with your other head unit. The issues of how you run the empeg are whether you use the other unit as an amp, or which unit gets primary use. You have to get an external amp if the other HU is going through the AUX inputs of the empeg. Alternatively, you have to make sure the HU you're buying has AUX inputs (but I don't know about this, I've never replaced a HU before the empeg).
2) on other upgrades, it's really your choice. I already mentioned the external amp. An amp is also good for getting excellent sound from your system. Every system I've heard that has an external amp is much better than those without.
Likewise, a subwoofer adds alot to the experience. I don't know if your factory system came with one or not, but I can't imagine living without mine. I strongly suggest it.
Good luck and welcome to the board!
DiGNAN