Temp sensors are engine (ECU fuel) under manifold, Air temp in the manifold near the front and Fuel temp sensor within the FIP under the top lid. Before the FIP was moved did you carefully scratch a couple of marks on the pump ? This adjustment is very small and the ECU has to adjust, everytime. It's not like ignition timing. The adjustments are made and you really need the right test gear. Try to locate the engine number and that may give an indication to it's type. Although I do not think it would matter too much. Timing a pump can affect it's fueling if it's retarded, but you can pick up timing dial gauges on the web now. You need to follow the RAVE manual. Moving too many things, leads to a build up of problems. Logical process is required. Did the engine come complete with the pump ? When you undid the pumps top, lifting it too high can let the control collar spigot pop out and problems there. Search youtube for Bosch VE EDC pump overall . There's a video with a Bosch tech pulling one apart also VW Turbo Diesel pump seals, they show the spigot.
Engines are Early EDC and yours was a late edc. You would need to check RAVE as to specs on the timing.