Hi Padders,
As you are building a Special with a collection of various parts, I understand why you want to alter the stanchion length to get the bike sitting "right".
I had overlength Marzocchi's on my first Jota so had them shortened at the local machine shop. I took the chrome tubes in, and he shortened and re-threaded the end where the alloy stopper screws into.
Fairly simple procedure for him, and as he had two to work on, there was always a reference for him!
As long as you are 100% certain that you are shortening them by the right amount

and you avoid the middle exhaust hitting the mudguard under braking

the job's a good 'un.
I'll be getting the Ceriani stanchions done on my 3C project as soon as I've worked out the right length - I deliberately bought NOS 610mm ones so I could raise and lower them until I found the right height to balance the altered rear subframe on the bike.
Chris
David Burton Engineering 01253 868111 did mine, but I daresay there are perfectly good places nearer to you