Fuel System Problems

I recently was advised to clean and flush my GU Patrol fuel tank and lines to clear of suspected sediment. I took my patrol to a local mechanic and aske them to provide this service, which they agreed to do.
At the time I also asked if they could install a fuel filter that has a glass sediment trap on the bottom of the filter. I had seen these on other Patrols and thought was a good idea so as I could see if anything was being caught.
The job was completed and I paid for the job.

Problem 1. When I picked the patrol up, I noticed the "Sub Tank" light was illuminated on the dash. I also noticed the sub tank selector switch would not light when I pushed the button. There is fuel in the sub tank and it too does not seem to being used.

Problem 2. The fuel filter I asked to be installed was connected in series with the factory fuel filter. They mounted it about 2-3 Inches above the factory filter, just in front of the brake master cylnder on a bracket. The problem is now when the car is parked uphill on a slope of more than approx 20 degrees, the patrol will start then stall. I have to open the bonnet and pump and prime the fuel up to get the patrol to start. if I park on flat ground or downhill, I do not have this problem. The fuel pump now seems has a wierd ticking, vibrating sound, especially after priming the fuel.
I took my patrol back to the mechanic and he not sure of what the problem is and says he hates diesels for this reason. I need some assistance to solve these problems so I can tell him what to do!!