Pointless to remove the FX loop. The Ceriatone loop is a simple "interrupt" FX loop. When nothing is plugged in, the circuit works EXACTLY like the loop wasn't ever there, you gain nothing by removing it except some leftover holes.
But to remove it, it's inserted between the middle lug of the Treble pot and the .022uF cap before the phase inverter tube (V3) tube.
http://ceriatone.com/images/mods/FX-Loop.jpgThose wires get snipped and replaced with a jumper that runs from the pot to the cap.
For the Master Volume? This is stuff, it's not quite as unobtrusive as the FX loop. If it's a Post-Phase-Inverter Master Volume (PPIMV), I would say, "keep it." On "10" it's like it was never there and if you need it (very few venues can be played with out attenuation these days), it's tone will be as good as any attenuator, power scaling or other solution. You can tell a PPIMV because it'll have a dual pot in the chassis, one for each side of the power amp push-pull set-up.
Even if it's not a PPIMV and just a typical pre-PI MV, I might or might not remove it. Ultimately, that's key...why do you want to remove the MV and FX loop? In what way are they bothering you? If you have a legitimate, present gripe, then remove away. But, most of the time, people go in and spend time and effort undoing things because of some bullshit, amp-purist hype about how these things are detrimental to tone. In some cases, they can be, but for most part, not using the feature is the same as not having the feature.
I can't tell you how to remove it because there are a good dozen different ways to install one.
But compare you amp to the layout and this schematic and you should find where the extra parts were installed...
http://www.raw-sewage.net/images/jtm45.jpghttp://ceriatone.com/images/layoutPic/marshallLayout/JTM45ceriatone.jpgHere is Nik's PPIMV mods he posts about...
http://ceriatone.com/images/mods/Type-2-MV.jpghttp://ceriatone.com/images/mods/Plexi50LeadPPIMVFrontCeriat.jpgI believe pretty soon, Nik is only going to be building models with these features stock.