Delayed fuel injection should not cause Carbon Build up on the air inlet valves. The only way that I can see this happening is if the air inlet valves are still open while fuel is being injected and burnt!! So either the injection timing or the valve timing may be a long way out.
I would suggest putting everything back to the original Test Bed or Workshop Manual Condition, something is very wrong with your engine.
The Carbon on the inlet valves may be caused by leaking oil seals between the valve stem and the valve guides. This could easily cause Lube oil to be burnt onto the valve, stopping it closing completely and allowing exhaust gas to blow back into the charge air manifold, this would raise the charge air temperature and reduce its Oxygen content which would cause high exhaust temperatures and turbo charger surging, low compression pressure and low peak firing pressure. It could be that all your problems are with these oil seals rther than with the fuel pumps. These seals should be removed before lapping the valves in and new ones fitted before final assembly. Sometimes they are an "O" ring fitted in the bore of the valve guide, sometimes a "Gako" or "Garter Spring" type seal on the end of the valve guide
I would also suggest that you try to inspect inside the air manifold and air cooler, if the turbocharger is "surging" this is caused by the air manifold or scavenge pressure being so high that air flow over the air compressor wheel stalls and air flows backwards, from the manifold through the turbocharger and out of the air filter. This can cause heavy fouling of the air coolers, which should be chemically cleaned regularly. I would suggest that you try to measure the air manifold temperature close to the cylinder head, it should be the same as at the air cooler outlet, if it is significantly hotter than exhaust gas is blowing back into the charge air manifold or scavenge space.
I assume that we are talking about an engine with a single, individual fuel pump for each cylinder? Could you give us some more information on the type of engine?
Good luck with this one.
It is always better to ask a stupid question than to do a stupid thing.