There should be significant “harmonic differences” from the BJr, especially if the Billm mods have not been done. One of the coolest things about the Two Stroke is how harmonically rich it is. I found myself using less and less effects when I got my first Two Stoke going.

One thing you might try: because it appears that you have plenty of lead length left on the OT, try moving it closer to the middle of the chassis (away from the input jack) and see if it helps clean up the signal.
There should not be any down-side to moving it closer to the PT, but moving it away from the input and preamp section might help.

BTW, the Billm mods really transform the BJr into a great little amp.
I’ve modded a number of them and they all sound so much than stock.
Many times people change out the speaker trying to get the BJr to sound less boxy, but it’s really the flawed bias circuit that’s the cause.