AFAIK, the main difference is '68 marked the year when Marshall started using a "split-cathode". It meant the V1 tube channels were truly independent, so the Treble channel remains bright and more gainy at high levels. The channels in previous shared-cathode design actually sounded the same when turned up. I think that was the only difference. After '68, the preamp section became brighter/tighter and more gainy. The shared-cathode meant the same preamp spectrum & gain signature could be reinforced by ~6dB, so the next gain stage could be driven harder. It's a fine point, but part of the deep overdriven sound that could be too dark/dull with EL34 tubes. If you go with a '68 spec, consider using JJ 6CA7 beam power tubes biased to ~75% of 25W dissipation -- fat shimmery cleans and a deep overdrive roar with better clarity and even to odd harmonic balance than EL34 pentodes, and less of the shrill mash of 6550's. The JJ KT77 are another great full clear beam power tube, but better for a modern Metal sound in 2203/4 designs.
Either way, I'd mix some short and/or medium plate preamp tubes with a long plate in the PI slot for a full balanced dynamic sound. The low noise med plate JJ 'ECC83MG' and the long plate 'ECC803S' are actually great inexpensive choices. Some prefer the more mushy/grainy Sovtek 12AX7 LPS in the PI. Valve Queen sells the long plate Ei '12AX7 NOS/NIB' that might be worth a try.
Thanks ... Smallbox 50W format is a bit more attractive to me but if I can get a bit more preamp saturation from the SL68 then that might be something to consider.
In either case the plan is to hit the front end with boosts, od's, fuzzes ... etc. and get most of the high-gain sounds that way.
If you aren't already aware, for less than 1/2 the price of an SB 50W (less if you order as a kit), Ceriatone makes a great turret-board wired 'Plexi50 Lead' with a passive FX loop, half power switch, Bright cap switch, and amp voicing options from '67 = shared-cathode/bass to '73 = split-cathode/lead: http://www.ceriatone.com/british-style-plexi50-lead/
You might want the more aggressive '69 voicing, but you can always drive a '68 harder with pedals if you prefer the softer filtering. I think it's very easy to change anyway. I'd order one without the OT if they will offer a discount, and get a Classictone OT to install. The stock Ceriatone OT's are apparently not made with the best Steel. Reports claim they compromise fundamental note clarity/punch, and are more fizzy (low level distortion). If you are confident wiring in all the Iron, you could order the Ceriatone Kits: "Pkg 1 w/assembly", and a Head cabinet. Then get a Classictone PT, OT & choke, and your own tube choices for virtually the same price as the fully assembled head (but less shipping cost). It might take ~1 hour depending if you have to punch/drill any holes.
You can pay a lot more for Marshall Iron, but audible improvements are dubious. Merren is supposed to make the best Plexi Iron. I think the owner is a bit "eccentric", so I'd keep it simple and direct. Amp builders generally love Classictone, but go for the Merren if you are concerned. Should be ~2x the Classictone price -- maybe a bit less: http://www.merrenaudio.com/home
The hotly-biased JJ 6CA7 tubes might be best with the '68 voicing and the more clear OT. That's the early EVH sound anyway. The EHx 6CA7 have a sort of cardboard overdrive quality. The JJ are more glassy/hard, but biasing them hot smooths the top end and adds even harmonics for a richer sound -- like a tighter/smoother 6L6GC. They are also very tough, and should last years, even biased hot. EL34 tubes actually tend to get wild and cause catastrophic damage when driven hard, depending on the socket wiring. As with newer Marshalls, Ceriatone might use a high socket resistor value to prevent that, but it affects the tone/dynamics. The JJ 6CA7 can handle the Traynor amp style pin 1 "raw bias current" mod. It keeps the tubes more stable without affecting the sound, but precludes the use of most beam tetrode power tubes. The EHx 6CA7 can not handle that mod, but I think beam tetrodes don't go wild anyway, so the stabilizing mod isn't even needed, and the socket resisters can be lowered to original values without concern. I'd go with the JJ 6CA7 (if you don't go EL34) and the preamp tubes I mentioned. A full sounding dynamic Plexi with separate channel inputs is a good pedal platform. The big clear JJ 6CA7's should enhance that.
A "Bass" tone stack might actually be better in some ways -- deeper bass and cleaner midrange. It could be put on a switch with a simple/cheap mod. That might be a fun little project, and you may discover some other useful mods in the process. You might consider the 10%, 1/4 or 1/2 power mod. It sends some output to ground via a big resistor on a switch, and doesn't reduce dynamics like the "Half Power" (triode mode) switch. Part of the classic Marshall crunch sound is from the second preamp tube being biased cold. That could be easily put on a switch as well if you want a less grainy gain path for your gain pedals. This site has mods like that and many more: https://robrobinette.com/Generic_Tube_Amp_Mods.htm
Maybe download the Ceriatone Plexi 50 manual. You can probably specify some different audio path caps. The yellow Mallory 150 caps are actually warmer and smoother sounding than the TAD Mustards, even though they are cheaper -- probably just less resonant and better shielded or something. They might be better for a pedal platform amp. Amp designer Randall Aiken recommends Polypropylene caps for the temp stability, long term reliability, and tonal linearity for most audio signal positions. There are serval brands that offer the axial pin format for turret boards. They are generally about the same cost as TAD Mustard (metalized film) from Mouser. I'd ask Ceriatone about using them. Aiken also recommends Silver mica or polystyrene film for pF value caps for their linearity. Again, a smoother high end might be better with a glassy sounding power tube like the JJ 6CA7, and the overall clarity should make the most of your gain pedals. Lotta hype in electric guitarville, and lotta opinions on which caps sound better. James Marshall used what he had on hand in his amps. I'd just use the most-reliable/accurate caps for the money, and make changes in values and placement to alter the tone/response if needed. Then again, it may not be worth the hassle to source Polypropylene caps for the subtle difference it may make, and considering that all the heat emanating from a Marshall head is above the circuit board.