Hello mate
I'm not going to go into any non-dodgy (!) specials I may or may not own, but in my limited experience the DVLA are utterly useless, so if I were you I'd first off just register it as the original Honda, back on the road after a break. ie, state the honda engine number on the document. This would get it into the system without too much fuss. If they wanted to inspect it, tell them its not finished yet. I'd also do all this by written correspondance, seems to get a better result than the "Computer Says No" folk on the phone. And Emails are too easy to lose/ track/ discard. Keep photocopies of all letters.
Do this soon, as it may take a while, and also the following would take a while....
When you get the original V5 reissued (as a V5C i think), then a week or so later, send it back for an engine number change, probably with a covering letter stating a yamaha engine has been put in (you've just decided on it...). on the form, just put the Yam engine number in the frame, I don't reckon you'd need to state "yamaha motor". This makes it easier for them, and they'll probably discard the covering letter and hopefully just put it thru the system. I'd keep a photocopy of this (dated) letter, so that if any trouble arises in the future ("You didn't tell us X ot Y...") you can wave your letter under their nose.
I know the forks are changed, but the theoretical bike you're building so far only has an engine change...
Then, the next week, you theoretically change the front end and wheel. There's no provision to state this on the V5 document....
next, tell them about a colour change if you want.
All of the above would be to try to avoid the inspector coming round!! Of course if they want an inspection, you'll have to be a bit clever, but if it looks ok, then will he be so much of an expert to notice a non-standard fork? Mine have never been inspected, so can't offer too much advice there... So yes, I'd try to blag it!
Re insurance, my model is a "special" on the document, I told them about non-standard parts etc.
However, I advocate none of the above and all of this is only for theoretical discussion!!! Can anyone add to this? Or is this *REALLY* bad advice?! Not had to deal with this kind of thing since the advent of the mass computerisation of the system. Maybe when you go for MOT it wouldn't be on the system??? Dunno MAybe as its been out the system for so long when they scan the barcode it will need a manual input of data anyway??
best of luck, hope to see it!
