I simply replaced the three directories (by first removing the old ones) and copied everything else into my dedicated server... and it loads.
However, it appears that the mods are wrong. Specifically:
client (1.0.98) has:
Merchants-1.1.3
TFCTech-0.2.10-A6
TFCUdaryMod-0.2.31
Buildcraft-7.1.16
buldcraft-compat-7.1.4
etc.
server (should be .98) has:
does not have merchants
does not have TFCTech
TFCUdaryMod-0.2.30
buildcraft-7.1.14
buildcraft-compat-7.1.3
etc.
I confirmed this by looking at the dedicated server download directly. And no, I didn't look at everything because I figured you already figured out it's the old dedicated server download
I tried just copying the script, mods, and config directory in and that didn't work. I figured that would be the case because the server code would not contain the new stuff. I was right... (based on the classes not found errors)
Is that already uploaded and we are just waiting on it?