This is the kind of nonsense we go through with HD motorcycles all the time. FWIW, HD motorcycles (pre '70 or so) had only an engine number. which is stamped on the left side engine case. So let's take a look at this example: Custom builder has remnants of a 1952 Panhead engine, cases with "52EL2210" and no title. he is in New York (no titles issued prior to 1974). go to local DMV or State Police office, run the number to verify that there is not a certificate of destruction or reported theft of 52 HD with VIN 52EL2210. Go home, get bill of sale from anyone for 52 Harley with that serial #. Go to DMV office and file for registration only using bill of sale, and affidavit that original paperwork is lost, and that "bike" was legally obtained. Pay sales tax on $1000, or $1500. and be honest that it is a basket case. Build your custom, keep receipts for Frame, swingarm, transmission, forks. (any or all could have serial numbers) When you are finished, you have a legal 52 HD. In NY title will not be issued for pre 74 vehicles. If you need a title, take your transferrable registration to a "title state" and file for a title and registration there. in many cases you will need a VIN # verification. The engine number attaches to your registration / title and is officially the VIN. any other numbers on serialized parts (remember your receipts, and original receipt for tax paid) may be listed in the database of the state issuing the title as supporting documentation. Now the sticky part, since you have multiple serial numbers, some jurisdictions may brand the title as "rebuilt wreck" in which case you still would have a 52 HD. If the state decides that the bike is "Assembled from parts" you could get a title with a state issued "ID number" (essentially a VIN) which would make the bike a 200X Custom, not a 52 HD. then your modern safety/ noise/ emissions requirements would apply.
This all being said, I'd assume that Rods should be treated in a similar fashion. If you have documentation for a particular VIN, you should be OK. If you build a kit, frame or not you will have a certificate of origin and it should be treated as a 200x custom. Moving a VIN to a different frame and body is not rodding the original and should not be treated as such. Building a rod around a chassis and firewall with the VIN in place, regardless of the running gear should give you the original documented year, make, and model regardless of the other parts replaced.
Bottom line, California is a socialist state and will do anything to squeeze money from the population hiding under the banner of "for the common good"