I would always check with the manufacturer or supplier of the power transformer as to whether it can support the power tubes you want to use. But I would say that if the PT can run EL34s it should be fine with KT66s.
My only reservation with building anything with KT66s is that good KT66s are difficult to come by. Jjjimi is spot-on though when he says that a JTM45 will have a BIG clean sound. And his recommendation of Valve Storm is spot-on as well. The chassis and hardware from Valve Storm are as good as it gets. You can use KT66s, EL34s or 6L6s in a JTM45 usually. I like KT77s which are like a really good EL34.
I've built the TMB MV 18W amp from Trinity and it's not bad but not as big a sound as the JTM45. As Jjjimi says though you can get it sounding good at potentially lower volumes. The other Marshall I would look at - and it is louder again than a JTM45 - would be the 1987. When built in a '67-68 spec it is one of my favourite amps. The low end is more solid than a JTM45s, which can get a bit flabby with extreme drive. It has beautiful cleans if you link the channels with a patch cord and when cranked there are few better sounds in rock'n'roll - and few places you can play that loud unfortunately. But it does take pedals well.
As a pedal platform, a great gigging amp, and something with exceptional clean tones I would recommend something like a Fender tweed Bassman built as a 2x10 or 1x12. You can buy kits for a 5F6-A Bassman and put the chassis in a range of cabinets - Mojotone could probably built you a cab with both a 2x10 baffle and a 1x12 baffle, for example. I have built a few 1x12 Bassmans with Mojo cabs and they sound awesome. After all, the JTM45 was heavily based on the 5F6-A Bassman. The Bassman sounds sweeter and the JTM45 a little more rock, but for the volumes we generally have to play these days the Bassman is possibly a better all-rounder.
