I have to note that my modded twin and my SMS sound kinda different. I like my SMS much better, it is focused and has been sounding better and better the more I play it. I have put some hours on it now, and I play it in a band setting about 4 times a week so it is breaking in nicely and quickly... I had to switch back to my twin for a couple of rehearsals and gigs and the difference was notable.
The twin has more emphasis on the highs and high mids than the SMS, which is something I don't miss.
The mac and the JBL's round out the tone proper, IMO. The SMS is very different through different cabs and amps, so the proof is positive. Those components are KEY in an analog system, I agree JBL E's are much easier to push and not worry about, my K-110's are brighter, but I have been warned a few times about their fragile nature. The E's sound just fine, and are actually Jerry's speaker of choice anyway.
Of coarse the guitar too with proper electronics. I promise a MC250, SMS and all the other killer gear you have will throw you where you want to be tone wise. You have a good Jerry feel and guitar, this would be like a ton of bricks once you try it. Aren't there some friends up your way with a rig like that you can try? That would be helpful. I have to say I like my MC100 better overhead wise, but I have yet to really use the full power behind it, and the MC250 gets PLENTY LOUD! Plus I like the fact the MC250 doesn't need fuses.
You are on the right track, If I was to build a Jerry rig for what I do and where I play again, I would use the same thing I have the second time around too. It just works!
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