Such as how to hook up the serial port from the sleeve to the box... as in would I need to hack the wiring in any way? (I remember something about the serial connections not quite being designed right on the sleeve)

IIRC, ground isn't connected in the connector... Propably neatest to
unsolder the existing connector and route the wires to a chassis
connector. You'll probably want to increase the speed of the serial
connection to 115kbp in docked mode too - edit the init.conf file.

Another question is about cooling... any suggestion on a way to keep the empeg cool in the box. I am thinking a few slits in the sides/top/back of the box with a CPU fan on top of the sleeve, one thing I am wondering about would be the power hook up... can I just run the fan from the amp remote line on the sleeve to get the fan spinning?

Sounds reasonable... IIRC the remote line doesn't like more than about
1A pulled from it. Probably a better idea to let the remote line control
a relay that powers the fan from the power supply directly.
Don't forget a free+wheel diode across the coil of the relay.

/Michael