Well done on getting your bike back.
1. Unless you can restamp the VIN on the headstock really
neatly it'll always look suspicious. I'd be more inclined to get an aluminium VIN strip and epoxy it in place. If you can't find anyone in the US that'll do it you can get one here in Australia.
Here's a place in Australia that can make one for you. https://www.niddrienameplates.com.au/contact
Ask for a Motorcycle VIN Strip (they do 2 sizes one for cars and a smaller one for bikes). And make sure the VIN is quite clear in your communication with them.
In addition to stamping the blank riveted plate with your VIN you also need to identify it as a T500 series. I've attached an example picture but the US plate may be different.
Don't worry about the engine # not matching the VIN, they never did.
2. The cable for the seat release hasn't changed for years. Used on most 955 models and 1050s. Should be easy to get from a wrecker.
3. The wires to the ignition switch being colour coded shouldn't be too hard to fix unless they cut them right at the solder terminals.
4. Don't forget the tail fairings are common to both 955 Speed Triple (2002 - 2004) and 955 Daytona 2002 - 2006) so that should help your search. Widen you search description to include terms such as 'rear fairing', 'rear panels', 'ducktail', 'tailpiece'. The black mid panels are aslo common to Speed Triple and Daytona although a lot of Daytona ones are carbon fibre (effect?).
5. Union Jack Decals - good luck finding originals. There's a paint shop here in Sydney that can replicate them if you can't find any locally. Let me know.
Oh, and document everything so that if you sell the bike you can be open and honest as to why the VIN appears not to be original.