Starting at the top, as far as I'm aware so this may well be wrong I thought the manufactures and teams wanted to run to superstock and supersport rules as it saved them building special bikes just for the TT.
There would be no point in having the superstock race if you didn't run to the class rules as everyone would just run a superbike.

Be careful quoting FIM regs.
From TT regs; Machines must comply with the2008 MCRCB Supersport Regulations.
From MCRCB; These are the technical regulations of the MCRCB and in principle follow those of the FIM, in case of clarification the FIM regulations may be referred to, however these regulations take precedence. If you are competing in FIM events you must follow the regulations as stated in the FIM Road Race Technical Rules, as they may differ.

Lets also be very clear as to what we are talking about as superstock and supersport rules are very different. supersport allows quickshifters superstock doesn't unless fitted to the homologation bike.

As for engines it doesn't mention anywhere that I've seen that engines must be of the same year. Only that they must be to homologated standard as such if the engine hasn't changed from 06 to 08 then that's fine. I agree FC that if any one part changes the bike need a new homologation however is the engine number prefix is the same and it's specification is the same as the later one why can't you use it? Let’s also remember that the homologation bike may not be exactly the same bike on the web site. The manufactures are not daft they will put through a bike that will work best for them.

As far as I can tell from reading through the rules quickly there is nothing that anyone has mentioned in the thread that is illegal. Some things that may not be in the spirit of the rules but nothing that's illegal. In my opinion all these people are doing is exploring every possible avenue available to get a competitive advantage. At the end of the day in may ways some of these things are no different to what Bob Heath used to do at the classic manx or Brian Read when he changed tanks in the pits during the Junior TT, not illegal just bending the rules to the limits. I could list many other occasions like this.

Not sure where you read the shock bit steve from MCRCB sstock regs; Rear suspension unit (shock absorber) may be modified or replaced

So is the bike legal, impossible to answer without knowing what the homologation spec is.