I think I wrote earlier that I will keep the S2 lights… 
Not sure I understand. You are referring to S3 taillights? While the S2 were red/amber, S1 were all red. S1 and S2 lenses interchange.
Boring anecdote (sorry): My 73 S1 came with red/amber taillight lenses (and bootlid plinth) that would be carried into S2. The Missouri state inspection station rejected my taillights because they were not all red, as required by law. I replaced them with S1 lenses. Then I realized that the amber portion emitted red light (due to an internal red filter) and was therefore legal. But I didn’t fuss, as I preferred the appearance of the all-red lenses anyway.
Either wrong or market depending. I know both in the S1, but I think they were red in the us until some point.
I agree either S3 or S2. S2 lights and S3 plinth should work nicely (My favorites are S3 and S1 early, with integrated reflectors but those are hard to find).
I believe cutting square holes in the S3 lid would be straightforward! I thought you were counting the holes too when you said you had at least 17 holes to finish (don’t know much about golf).
In the US, S1 taillights were all red until 1973, the last year of S1 production.
An amusing Jaguar factoid: The early S1 Daimler bootlid plinths were fluted and quite long. They replaced the “wings” on early cars and did not contain lights. Later S1/S2 Daimler plinths were similar but did contain number plate lights (which were removed from the bumper). These plinths had more fasteners than the Jaguar S2 plinth, which was shorter. However, when Jaguar introduced the sleek S3 plinths (smooth for Jag, fluted for Daimler) they used the same mounting locations, and the same rubber seal/embellisher as were used on the earlier Daimler plinths. But as mentioned the lock is quite different.
A Craigslist ad for a S2 lump just appeared in the LUMPs thread. It has S3 flush door handles, and an S3 bootlid including the narrow plinth. Looks very nice. Could have modified an S2 bootlid I suppose (welding up the reversing light openings; figuring out how to fit the S3 lock).