hey fuzznaut - here are some things i can say that may hopefully provide some insight and help. let me take your questions one at a time. i looked at the build notes, and if you want it to sound like the one in the video take Sensei Tim's advice, since that's him in the video.
1 - the mods suggest, as far as removing the cap, should be just that. take them out of the board, and don't replace replace them with jumpers. what you can do, since i did not build this yet, is you can put sockets in place of where the components are supposed to be that you're remove, and try it with nothing there and with a jumper to see how it affects the circuit. if you put a jumper in and it doesn't work simply pop it out of the socket, if you need a jumper just pop it in, no need to bust out the iron.
2 - in order to identify where certain parts are you need to use the schematic, so Sensei Tim mentions removing the 470pF cap in the input stage and preamp stage. luckily in this effect there are only 2 470pF caps, but that may not be the case, like the 10k resistor you mention. i don't have the schematic currently, but i think that the 10k resistor to the left of Q2 is the one that needs to be changed.
3 - i haven't seen the layout posted on DIYSB, so i can't comment about the similarities between the one mark posted and the one at DIYSB. if a layout is verified here, then you can rest assured that it will work, and if there's a problem there's something going on in your build.
4 - as far as motterpaul's comment about j201's, yes they can be a bit of a pain, as the through hole ones had terrible tolerances. having 100k trimmers provides enough leeway to get correct drain voltage, there's nothing wrong with the value, don't change them.
5 - while one pot affects the other in a marshall style tone control, it's not going to be that drastic unless one pot is wired backwards, so if the mid pot is backwards and you think you've dimed it, and it's actually removing all the mids, it still shouldn't get shrill.
it's hard to tell what's going on as far as the issue with the build without any pictures of the board and the components. if you can take some good resolution pictures of the bottom and top of the board, as well as your wiring.
i would check for the following things.
1 - run a thin sharp knife between the strips of copper to ensure no solder bridges.
2 - use your DMM to check for cold solder joint. put your DMM into continuity mod (the one that beeps when there's a connection), put on lead on the copper track and touch the other one to each solder joint on that track. if you don't get a beep then the joint is bad, remove it and resolder.
3 - check that your transistors are correctly inserted - sounds like i'm being a dick, but it happens to us all, and a lot of us, including me have debugged pedals for awhile until we realize that not only are the transistors inserted wrong, but they're not even inserted.
4 - then check your wiring to make sure that things are wire correctly.
5 - make sure nothing is grounding out - board, components on the board that shouldn't be grounding, jacks, etc.
6 - check for correct value components, especially around the tonestack, input and output caps. those are going to have the biggest impact on the amount of bass you have running through and coming out of the circuit. i have had an experience where some caps fell into the wrong compartment of my cap storage box, so what i thought was 470nF turned out to be 4.7nF, needless to say it turned the pedal from sounding like crap that didn't sound right to better then expected.
in my experience it's usually the stupid, little things that cause the biggest problems in a build. i gave the steps i personally take when i debug my pedals, and hopefully you notice that i go from simplest solution to most difficult. i test after each step, this way i don't waste time doing the most time consuming things unless i have to. if i have to go through and check each component i get super meticulous and not only check using the markings on the parts, but also test with my DMM for their actual value to make sure they're correct.
let us know how it works out. i really hope you get it sorted, as i think this should be one of if not the best sounding JCM800 sounding pedals, at least that's what i can tell from the video.
edit - i just saw this posted by Sensei Tim under the build notes "I think it was the 10k on q2, but I can't remember. You could always socket both of them and see what/if there is a difference."
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