Hello, I hope the following is of assistance.
Yes you can replace the EPIC pump system with a Bosch manual system. The automatic transmission will make no difference as the A4LD transmission isn't electronically controlled.
You need to fit a new throttle pedal and cable, the mounting is the same for the EPIC pedal so this is a straight swap. The fuel pipes are different fittings on the pump and the injector pipes are different so use the Bosch pipes.
The immobiliser system needs the fuel cut off solenoid on the new pump wiring direct to the ignition, you can blank the EGR valve if required with thin aluminium.
The best pumps to use are either 0460-414-145 686-2 or a 146/686-2 but you will need to adjust the pump timing to account for the turbo boost. Make sure the EPIC system throttle butterfly remains open. If there are any problems with the temperature gauge there should be 2 sensors on the thermostat housing 1 for the EPIC system and 1 direct to the cluster.
There are many people who have completed this conversion so it should be easy enough for you to do, further information you could try http://fordtransit.org/ where many people have done this conversion themselves.
Let me know if I can advise further and I'll reply as soon as I'm able to.