As Bill says the Dessalator is a good design. There are parts available and support form Amel and the Amel Owners Group, I would suggest sticking with it and doing a ground up rebuild
When I bought Annie (SM37) the previous owners had not used the watermaker in over eight years so it was a known project. I suspect your watermaker may be in a similar state. The good news is that it is fixable with a little bit of time and patience. I recovered my watermaker replacing the membranes, the membrane endcaps (precautionary as they were original and had stress cracks) and the high pressure hoses(also a precaution). The pump needed to be disassembled and cleaned before it would build pressure but it was pretty easy to do. Once back together she ran fine. It sounds like your pump is functioning so you are probably good there.
The worst issue with the Dessalator was the early control system which as you found out does not actually test the water quality. I deleted that whole bit of junk and test the water myself before sending it to the tank. I currently have the product water discharging to a free hose that I allow to flow into the cockpit when the unit runs. I sample with a portable TDS tester then put the hose into the fill nozzle when it is good quality. Nothing goes into the tank without monitoring. I think Bill suggests doing that somewhere below. That is the best way to ensure your getting good water. And that can be very important if you are underway relying on your tank for potable water. One bad batch from the WM and poof you have no water at all.
To get SW into your tank you either have a bad o-ring or the membranes have been damaged. Ether way replace the membranes and o-rings and you are good, and will know for sure the condition of the membranes.
I installed my membranes in 2017, they are still running just fine. Run the WM every once in a while for a few hours, never pickled it. If the boat will be idle, I flush them with fresh water.
Check the end caps on your membrane vessels for signs of cracking. I think Dessalator has new material available now that won't become brittle.
When you reassemble, watch your hoses when the unit is running, make sure they are not rubbing on anything.
Verify the pressure gauge is reading correctly. My gauge is not the red/green version but read in Bar. It is reading 15Bar higher than actual.
Change pressure slowly. Both up and down.
Run the unit with no pressure to flush the concentrated brine out of the system after you are finished making water.
I bought a solenoid valve to be able to test the water at the galley sample port and then flip a switch to sent it to the tank. That is a better solution, but I have been lazy.
Portable TDS /conductivity testers are cheap and available online.
Regards, John Clark
SV Annie SM 37
St Thomas USVI
A couple of suggestions