I have a PC-3000 switcher that is not working.
When I turn it on this is the message on the display.
"software upload mode"
No matter what I do I can not get the unit into any other mode.

I have purchased the service manual and there is absolutely no help there.

Does anyone have any experience with these units or know how I can fix it or how to upload the software?

Have you reseated all of the boards?

Here's the serial protocol/communications software. Which talks about communication thru the PC-3000, so see if you can communicate with it, via the com port.

http://www.curtpalme.com/docs/SonyG90_serial.pdf
http://www.curtpalme.com/docs/SonyG90_PJSerialCommSetup.exe

I'd say your firmware's corrupted, you might have to reflash it. No idea where to source that though...I'd say your only avenue would be Sony itself, not too many of these babies are out there.

...but I'd recon the Com port might be your only option at this stage.