So you cannot route sounds to Sub 1, which are labelled as outputs 3+4 on the rear?
I take it you can route audio to the main output in multimode and get sound from it but you get nothing from sub 1. You are also getting noise bursts from some or all of your outputs, including the ones that aren't working? Has the machine ever worked correctly?
Really sounds like you need to get your Emu looked at by a pro repair centre but considering the cost of a new E5000 it might even be cheaper just to buy a new one.
Here is a list of repair centres, not sure they all deal with E-mu equipment but I have used cimple solutions myself and can recommend them.
http://www.cimplesolutions.co.uk/
http://www.synthrepairservices.com/
http://www.synth-service.co.uk/
http://www.eprelectronics.com/