I also plugged my strat into the fx return to bypass a bunch of stuff and surprisingly (to me anyway) when I turned the fx return all the way up, it distorts.
Two thoughts ………………….. I've never owned or played any amp at all where I dimed all the controls. I don't drive my car with my foot all the way down on the gas. My opinion is that amps are NOT made to have everything dimed especially when you have a goal of a clean tone. Probably any of my current 3 amps will distort into an unpleasant tone IF I dimed everything.
I have certainly plugged into a FX return and enjoyed a very nice clean tone doing that. I doubt I had the FX return or FX level above 5. I've played my Larrivee acoustic thru the FX return and loved the clean tone it had. I've done that with several of my amps and enjoyed a nice rich clean tone with my acoustic. Same good results with each amp I tried.
So, …………… IF you did not have the FX return or FX level cranked way up and it still distorted. Then I'd say something significant is wrong in the wiring, tubes or OT or speaker.
IF you have another amp that has an FX in it. Try playing your preamp thru the power amp of the other amp. In other words, take your send FX jack and plug it into the return of the other amp. IF that sound clean to you, then the problem is the FX return or power amp on.
Another thing you can do is remove the FX tube and jumper straight from V1b into the LTPI. How does that sound? IF it's sounding clean and good to you, then the problem is the FX wiring or tube.
You're trying to isolate where the problem is coming from.
I've built several Tweed BluezMeisters and then Ryan's amp. All of them had a very similar nice clean tone and sounded much like the early part of that sound clip.
Something is obviously amiss and I'm confident that you can get this figured out.

Also check voltages, recheck resistor values and check for continuity. Carefully safely chopstick the solder joints and see if anything pops or crackles.
You might try a 12AY7 or 12AV7 in the FX. You might try a 12AT7 or 5751 in the LTPI.
With respect, Tubenit