Interesting setup. I also own a grey 250 clone, and I basically use it opposite to how you do, I use the built-in boost for a solo push and the pedal on 10/10.
To me, the pedal itself (provided it's a 250 grey clone) sounds much better dimed than the built-in booster (which is said to be based on the 308 circuit). Obviously it's up to personal preference, but I'm wondering if you tried it this way. Tell me what you think.
Incidentally, I've also read in a review somewhere that there was supposedly not enough gain on the built-in boost. I mean, really? Holy gain Batman. When I crank the built-in boost I can pretty much play the most obscene metal out there. In fact, I think there's more gain on it than one would need. I usually run it at 2/3 max if I use it as an actual gain boost instead of solo boost.
Also, KT88 demo is coming up when I get the other YJM heads. I think I'll keep one completely stock EL34. The other two will get KT88's and KT66's. I was thinking about 6L6's too, but I decided against those since they're not really related to the Marshall sound.
According to Nuke,Santiago has said there is MORE gain/distortion on the YJM boosted than a JVM 410!
I haven't been lucky enough to play a JVM so i've got absolutely no idea,just quoting before someone has a tantrum!