You need to be very careful when you sell this. Have it looked at by an old time TCA member if you can.
From what I can see, the latches that hold the motor in the engine have been painted blue. They are not supposed to be painted. Also, most originals have a pronounced wear mark where each truck has worn away the paint on the bottom of the frame in an arc. Yours shows wear that's a good bit less than I'm used to seeing. That leads one to question the overall originality of the whole set.
I would assume that the frame and steam chest have been at least repainted, if not replaced at some point. Look for manufacturers casting marks on the frame and steam chest and let us know what they are. Lionel did not make the cast parts, they farmed them out.
The engine appears to be a later copper trimmed engine, as it has the turned handrail posts instead of the sheet metal handrail "snivvies". Although it may be more common than the nickel trimmed versions, I always prefer the early prewar copper and brass over nickel. Personal preference, but I like it.
As for the cars, they look very nice, however, it's tough to tell originality based on some web pictures. I believe the dark vestibule cars to be early blue comet cars, and generally would have come with the cast journal boxes, usually, but not necessarily packaged with a 390E blue comet engine.
Restoration or major part replacement can impact value. How much depends on the work, and what agreement a buyer and seller can make. I would attempt to get an opinion from a non interested party, maybe someone that has one, and not an auction house or the train collector looking to buy a blue comet. To me, if someone has no interest in it, then you'll get an honest appraisal of its condition.
Then, represent it for what it is, and you'll be OK. Good luck.
