Head scratching, Puma 2.4 Limp mode, what to look for?

Ok, so removed turbo/intercooler hoses, all fine.
I decided to leave the inlet ports alone at this stage, as I agree that it's an easy way to introduce contamination.

I went for 3 drives today, logging everything, no problems, all ok, at this stage.

I have however ordered a new VCV/SCV from fleabay, Ford Transit MK7 VII 2 2 2 4 3 2 Tdci Fuel Pump Diesel Suction Control Valve SCV | eBay
From what I've read, even if this isn't the current issue, at least I'll have a spare when it does give up the ghost.
I didn't realise how common a problem these valves were. And after i found that jelly/silicone substance in my filter, it's only a matter of time.
As Pat said, best to treat it as a service item.

Just hope it doesn't happen too often, as I remember Pete from BAS saying there are only so many pump learns you can do before your ECU's EEPROM is cactus. I think the magic number was 14, on the 15th you need a new ECU.