Ok.....lets take it from the top. I call it as I see and anybody can correct me if I'm wrong.
1) Front cylinder: No view of the exhaust port. The exhaust header is SP2. It can fit on an SP1 exhaust port, it will have gas flowing issues in the long run, but it can fit. So this just proves SP2 exhaust header pipes. Nothing more.
2) Rear cylinder: same like the front. The exhaust header is SP2
3) This is NOT a steering damper mounting point. This is the hole that the lock pin slides in when you turn your key all the way counterclockwise pushing it downwards. Same on SP1 and SP2.
4) Same color on the clutch cover and the engine's RH crankcase cover indicates an SP2. The SP1 has crankcase covers bare aluminum colored. However they are identical in shape so it's easy to bolt an SP2 RH crankcase cover to an SP1 engine.
5) Oil cooler is SP2
6) Swingarm and wheel is SP2
7) Subframe is SP2
8) Front forks are SP2
From what I understand, unless you take off the cowls to check the engine mounts and take the tank off to check the throttle bodies AND take the exhaust header pipes off to check the exhaust ports themselves,
I truly believe you have a genuine 2003 RVT 1000R on your hands.
Don't worry about the VIN number which is mistaken for a CBR954. Honda was producing both models that year so the sequence of the VIN characters may apply on both occasionally.
You can only be sure with the VIN number if you run it with a Honda dealer in the Honda network database.