Offhand, I would reject B and D. I would take the entire cluster of caps in E and move them to the right and get the choke next to the PT. Those are your hum monsters. The caps themselves (eg; their metal cans) form a modest shield of sorts.
Do you have enough length to get your parts board kind of in parallel with the row of preamp tubes? If you are planning to use this long thin parts board designed for a long thin chassis, I believe you are destined to run yourself into problems with a more squarish chassis. In other words, do not only consider the big fat above-chassis parts you are planning on, take note of where that parts board is going to go. In the overall scheme of things, that board and its peculiar size and shape could be lots more influential than how big your trannies are and where you might mount them. A power trans for a 4 * 6L6 amp is about whatever size it is no matter what. Get my drift?
Your costs for all those can caps is going to be high. Those can be $15-20 each versus $1.50 each (times 2 to replace a dual-can) for PC-mount e-caps. The axial mount ones are quite a bit more. And they (the cans) sure take up a lot of real estate. And don't forget the $2-3 each for the clamps to mount those caps if those are called for. I can appreciate you may be looking for "a look" but you could get that with 2 or 4 of those cans above the chassis versus EIGHT. I myself would consider, at least, a cap board (or some physical structure producing a row of them, on terminal strips or separate turret/eyelet board) under the chassis. Something like the under-doghouse board in a Fender.
You're definitely doing the right thing playing around with possible layouts. Paper and ink is vastly cheaper and easier to deal with than metal and big holes that have to be neatly executed.
I have to tell you that I would consider a pre-punched 5F8 chassis from mojo or even some sort of adaptation of a Marshall chassis would very possibly make your life incredibly easier. Chromed, silkscreened numbers, right size, punched, done.