Both would be flexible amps, though if I were in your position I would probably be comparing a 5E3 with an 18 watt Marshall rather than a JTM 45 (the wattage/output would be more comparable). Also I'd suggest that building a JTM 45 with 6V6 output tubes will change the sound somewhat from whatever "classic" JTM sounds that you have in mind (Bluesbreakers w/ Clapton is my first thought).
I would suggest two things. First off, will you be able to deal with the volume of the JTM 45 that you'll need to get into overdrive? If not, a 5E3 or 18 watt would be a better choice. A master volume doesn't really help to my mind because then you're not driving the power section hard enough to get it to contribute to the distortion. An attenuator can work, but it takes a little treble off (at least when I use mine).
Second, listen to a bunch of Neil Young records and see if you like the overdriven/distorted tones, "Cinnamon Girl" or something like that. He's known for only using 5E3's, so you'll have an idea of what they sound like being pushed. Does it sound as good TO YOU as a Marshall? Got a preference?
Also I don't know if you own any pedals, but having one good fuzz pedal like a germanium
Fuzz Face or Tonebender can add a bunch of options for different levels of distortion. Since I started using fuzz, I find I'm cutting almost all my lead guitar parts with a fuzz pedal. Good luck!