Good info in these answers, I'll give my two cents of response at least.
The good news here is, the alternator and engine components being hot to the touch doesn't necessarily mean overheating, these parts run at around 90 degrees Celsius during normal operation which is easily hot enough to be uncomfortable for a bare hand, if you were touching them after the engine had been running down the road.
The engine very suddenly acting like the timing was retarded is a good description of what you are seeing, but it is probably not related to temperature. More likely something jumped in the timing system, especially considering you saw visible timing belt damage plus there was recent work done on the injection pump that you mentioned.
So there was recent work done on the injection pump, and at the time of that work there was no visible damage to the timing belt? And then someone did a repair, and a few thousand KM later, there is visible damage to the belt and the engine suddenly started running poorly?
Can you give more info on exactly what that repair was? Leaks? Did it involve taking the timing belt off?
To me it sounds like this van needs to go back to the shop or person who most recently worked on it. The recent repair is not a sign that there can't be an issue with the injection pump -- actually it is the opposite, it means it is quite likely that the issue was caused by that work. The timing belt might have been tensioned incorrectly, injection pump bracket moved out of alignment, or other potential causes. A photo of the belt damage would help understand it better. But either way, the story of recent work done and then this new issue is suspicious, even if the van did have a successful trip since then.
Depending on what pump was used, that may have something to do with this issue. Some people use 12mm mechanical pumps from Cummins or Perkins or Iveco engines that are too large for the VW engine and require excessive force to turn, leading to stress on the timing belt and related components beyond what they are designed to handle. That can make it more likely for the injection pump sprocket to jump a tooth on the timing belt, especially if the belt is not tensioned right or is physically compromised in some way, like yours has been.
That might be a factor in your problem, in the sense that I just mentioned above. But the lack of electronic controls isn't your issue per se. It would have been helpful to scan for trouble codes (start of injection) if you had electronic engine management still but since you don't, no need to worry about it.
Did you do the installation of the mechanical injection pump? If not, are you able to be in contact with the person who did, and find out what static timing setting they used? And/or, can you ask the folks who did the recent work that same question? If you can, then a good next step will be to obtain the standard mechanical injection pump timing tool set (dial indicator, holder, rod) and go through the timing check process. See if the current setting matches what it should, or if it's retarded. If it's retarded, then that's your issue.
Or, just take it back to the folks who were the last ones to turn wrenches on the engine.