HBP was kind enough to explain to me and give me a formula to determine what frequencies will be amplified with a combination of a cap and resistor. It finally sunk in that cap and resistors when used as cathode bypass is not a "brick wall" meaning it is not going to block anything really, it is just amplifying what you do want. You are focused on your OT which seems to be a nice one. Now you have it, but you are attempting to tweak your amp. Your OT will send to your speaker what your circuit dictates.
The formula is 1/(2*pi*Resistance*Capacitance).
http://www.vaughns-1-pagers.com/music/musical-note-frequencies.htmThis will show you the notes on guitar and piano and their respective hertz.
First try the simple things that have been suggested as you do not have any caps to play with. It will give you something to try until your cap order arrives. You are placing an order for some caps, right? Don't get hung up on the 4.7 as it is just one value. I mentioned going to mouser.com and order some 1.1, 2.2, 3.3, 4.7, and something in the 7 or 8 and 10uf. I get 50v. They are cheap.
Forget the Paul C. mod for now. It is just a common mod for princetons. I tried it in a 5e3 as well. It does help if you are looking for clean, but do it later as you may not want to. It deals with the PI and this is not where I begin tweaking.
Anyway, HBP told me to not try to restrict later in the circuit, but to amplify the Hz I want. You don't even have to use the formula, but if you do you will understand more and it will reduce tweaking time on future builds.
Guitar open e is 82.407Hz. Lowering the cap on v1 will get you closer to this and at the same time reduce how much you are amplifying lower Hz, not removing them. Remember, it is not a brick wall.
Just try an experiment. After trying tube changes and lifting the cathode you are not happy with what you get then use the layout I posted. Starting at v1 change. Check it and see if you like it better if only slightly. Moving left try another. Each change will remove a little more speaker flap and give you the ability to raise the volume with less breakup.
The way I understand it is it takes more wattage to reproduce lower Hz cleanly. That is why bass amps traditionally have lots of wattage. Amplifying lower frequencies than your guitar is capable of producing is a waste and often not very good sounding with guitar.
Continue this process until you reach the tone you want. If you make a change and do not like it you can either change it back or try something in-between. What I am saying is it is not written in stone, but I can tell you I have a 5e3 built this way with no trick switch. My OT 6k6. I have 2 different channels. The one I use for my telecaster is cap 4.7uf/820 ohms on v1a and les paul humbucker 3.3uf/680 ohms. Has lots of headroom, but someone who likes the tone of a stock deluxe would not like it. Works very nicely, but if you plug in an electric piano it does not sound very good in the first octave. It will play the notes just fine, but it is sort of thin.
It is actually possible to put on a "better OT" and you amp sounds worse because it is reproducing a frequency from your circuit better, but it is not a frequency you want.