The OP says the dirty residues are on the rear TB, the front one is clean, so it seems logical that the bretahing pipe from crankcase cannot be the cause of it as it points directly into the front TB...
Same boat here, a friends 990 is in the same condition, valves are in spec.
If it has residue, it must be a mix of things (fuel + carbon/oil...). Through the TB's things go only one way, fuel and air travel into the intake and combustion chamber.
These two do not produce residue, unless ver bad fuel and/or damaged airfilter, gasoline is used also to clean so its ruled out.
Only way to have it gunky is if anything comes up from the engine valves, and there can be exhaust fumes, unburnt gas, oil traces and carbon buildup.
For this to come up, either tight valves, bad firing/missfiring.. random injector malfunction can have it injecting at wrong times, or weak fuelflow that will have air/fuel mix not be burned due to lean condition...
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Raid de L'Amitiť 2011 RR (link