USB-serial has always worked for all sorts of things. I'm able to use minicom and hyperterminal just fine as well as flash other kernels including hijack just fine.

I'm using the upgrader that comes with emplode 2.0. I just downloaded the emplode for v3 firmware but it is only a zip file with the emplode.exe and emplode.map. I have copied these to the rio/emplode directory and am running the upgrade again but I think it only uses the empegupgrade.exe and doesn't care what version emploded.exe you have.

I am using the big disk builder from http://rtr.ca/bigdisk/builder_bigdisk.upgrade