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Sounds like it's coming from the EGR then. You can fit one of these :- https://www.ebay.co.uk/itm/183869556154?hash=item2acf7ac5ba:g:OaAAAOSw-DRdHK14 as long as you are ok with the extra NOX emissions.

I have a 2l Diesel 140 Estate which I have corrected the on board computer with VCDS. Previously it was about 8% optimistic, now it is fairly accurate, slightly under reads if anything. Did a journey from London up to Cheshire 2 Sundays ago, M1 / M6 170 miles. Set the cruise to 62MPH on the Motorway which was 90% of the journey & arrived home with 69 MPG for the journey, which I thought was quite good.

There are 2 sources for the clicking noise of stripped plastic gears. One is the EGR at the back of the engine, the other is the throttle valve on the inlet pipe just behind the radiator. Check which is making the clicking noise before you go further. Either will result in reduced engine power.

I have had a sort of vibration during acceleration, don't know if that is the same sort of thing as lumpiness. It wasn't always there but could be felt throughout the car intermittently. I had the bottom dogbone engine mount changed. The rubber bush had deteriated ( car has covered just over 200k miles so not surprising ) which allowed the engine to shunt back & forth too much. Only £16 for a new one & solved the problem.

This worked for me :- https://cardiagn.com/skoda-superb-ii-b6-workshop-manuals-owners-manual-wiring-diagrams/ Wiring diagram is down towards the bottom. Other workshop info also on there.

If you remove the small coolant pipe near the top of the coolant reservoir then poke it in the reservoir top. Start the engine, coolant should circulate through the pipe & into the reservoir. That will prove the pump is working. If no coolant comes out, either the pump is defective or the small pipe has a blockage.

" Trouble codes: P305200 - Starter activation, return message terminal 50 Short circuit to B+ static " Terminal 50 is the output from the ignition switch to operate the starter. I would start at the ignition switch & check you have an electrical signal leaving the switch when turned to the start position. From there I would guess it goes to a relay, then on to the started solenoid, but you will need a circuit diagram.

As you've got the turbo off, have a look at this video about the turbo mechanism. The control ring for the variable vanes is probably sticking due to a build-up of carbon in the mechanism. It's not much of a job now you have it removed to inspect & clean the mechanism.

What is the engine code of your son's car ? You will probably need an EGR emulator/ simulator or the ECU will detect the change & put the engine into " limp mode ".

It's sometimes a sign that the clutch isn't disengaging fully. Can you select reverse easily when the engine isn't running?

What is the engine code. You might be able to fit an EGR simulator/ emulator depending on the engine, then forget about the EGR & any faults it has.

If you are getting this overheat warning when the engine has just been started ( & obviously still cool ), you've had the coolant temperature sensor changed, I would suggest you have a wiring fault somewhere in the engine bay loom which is giving false data back to the engine ECU. Have a good look around the coolant temperature sensor plug & local wiring for damage, then trace the loom back towards the engine ECU looking for any chafing against anything adjacent to it. Check the engine ECU electrical multi-plug for any corrosion or moisture.

This seems to be the correct thermostat for your AQW engine. https://www.ebay.co.uk/itm/234340925912?hash=item368fcec1d8:g:iq8AAOSwuIxhvYdh As you say, it is rated at 88C.

So yes, just carry on as you did before. The regenerative braking has nothing to do with your friction brakes. I also often use gravity to bleed the brakes some times. As you say, it is slow, but there is no possibility of introducing other problems some of the other methods do.

I think this engine has a coolant cooled intercooler. These have been known to leak in the past, although it isn't a common fault as far as I know. If it is leaking internally, the coolant will be burnt in the engine & exit through the exhaust. The amount you are loosing probably wouldn't be noticed in the exhaust.