I'll have to defer to Marshall aficionado's to answer most of your questions. Hopefully Ritchie200 will chime in, as well as others.
I say that because while I once had a '73 50w Marshall (the "Model 1987" JMP Mk2), I haven't dabbled with them much. The 100w head is bigger than I could ever see myself playing.
... I have always liked Jimmy Page's tone over Pete Townsend's and from my little bit of research on the subject the beefed up PT in the Hiwatt has something to do with the difference in tone. ...
Remember Page used a LOT of things you might not associate with his sound at first.
But I think the Hiwatt is an entirely different amp, and its sound is more than just a power transformer. The Fane speakers are a big component of the sound.
Funny enough, at the same time I had the 50w Marshall, I had an early-70's DR504. I played those amps (and a Matchless Clubman) through a (maybe late-60's) basketweave 100w cabinet with G12H30's. Each of the amps sound similar enough when clean through that cabinet, though they each had their own quirks for controls and their own voice when cranked up.
I'd guess the speakers and output transformer, along with the overall amp circuit, will make the biggest difference in overall tone. Sorry, but I just lack the experience with enough Marshall amps to have an opinion about the different power transformers (and mainly output voltages) Marshall used in their amps over the years.
Also, could you please provide your opinion regarding M-50 versus M-6 iron as far as tone is concerned? Seems like M-6 would keep the PT cooler and also have more head room.
Mostly Greek to me... you'd have to ask the transformer builder.
My understanding is the lower the "M-number" the lower loss in the core. The transformer designer is going to be thinking from the standpoint of "power throughput" and designing the core size based on the power needed and the core material used. So I'd bet if they used a lossier material, they'd make the stack bigger to compensate. In other words, the M-50 100w PT may just be a bigger lump of iron than a M-6 100w PT, as the manufacturer adjusts for the increased loss.
I would think that I'd want the better, lighter M-6 core... but again, I'd have to defer to those who've built and tinkered with this particular style of amp more than me.
Reiterating an earlier point, I'd think the output transformer would have vastly more impact on the final sound than the power transformer, assuming the power transformer isn't grossly under-sized (like trying to make a 100w amp with a 20w power transformer).
... I was leaning towards M-50 because I am not looking for a lot of head room. ...
But you're gonna build a 100w amp?

You play stadiums a lot?
I saw Eric Johnson at a club in Nashville in the late 90's. Most of his amps were off the stage (or under the stage, I'm not sure which), mainly so he didn't kill people in the audience with the cranked Marshall for his lead tones.
Keep in mind Sluckey's plan has a master volume, which you'd dial down for preamp distortion. If you were gonna use the amp like my old 50w without a master volume, you'd have to crank the amp way up. Will that wind up too loud for you to use? The folks who've built Trainwreck clones (50w amps) talking about how brutally loud they are is what comes to mind for me.
Then again, I don't know your particular situation or needs.