1. With the Deneb USB card, if I install OS3.1, can I just bypass the joystick ports and use USB for everything?
Like said above, you can't bypass it, once workbench is started you can use it.
Early startup only lets you configure drives and if you have a PPC, you have a few more options.
2. Is there anywhere I can send the MOBO to get it fixed?
Maybe give Zetr0 a pm ?
3. Is there an easy process to bypass 3.1 and use UAE to install 3.9 to a compact flash drive if I get one? Is there a benefit to running 3.9 over 3.1? 3.5 and 3.9 seem to have mixed reviews.
Yeah you can start UAE and install 3.9 directly, but it will still require some 3.1 files.
I don't see any advantage on 3.9 other than a few updated librariers, performance wise I preffer 3.1 and than Classic WB 3.1.
Only thing I want to try is my Micronick 4000 with CS PCC to run OS4 classic.