Bottlehead proper will not be able to fulfill something like that. Kits are done in batches and you're asking for a custom order. Taking parts out actually can destabilize how things are packed and lead to shipping damage, so generally we just don't offer that option.
I provide construction services and can have a custom top plate milled (or an enclosure for that matter) that can hold the Sowter OTs and I can build your kit for you to use the #45. I would not, however, substitute the 6SL7 in place of the 12AT7s because I would consider that a poor design decision. Providing these modifications for an unbuilt kit isn't really something I'm adequately equipped to do.
If you'd like to chat more about the options, my e-mail is pb(at)bottlehead(dot)com.
-PB