THat is one of the most clear "original" schematics and layouts I've seen on the internet, most are badly scanned and copied.
The 5E3 "Deluxe" design actually does connect the volume control pots "backwards", in that the inputs connects to the wipers and the outputs taken off the "high" end of the pots. (this was not one of the usual "errors" in their schematics)
It looks like this was a first shot of mixing the two separate input channels, and the simple tone "Stack". It works fairly well, but the "taper" of the volume controls is kinda weird.
I'll try for a gut shot sometime, I'll have to remove the back panel, and get some light directed into the chassis depths in order to make it useful.
(My original under the chassis shots did not come out too well,)
The circuitry is simple enough so that point to point wiring could be done neatly, and with good results. I would suggest to just use one input jack per channel, for teh sake of simplicity and neatness. I would have left out the second inpuit for each channel, except that I wanted to make it as faithful to the original design as possible. A few years ago, I started a 5E3 build in a Grommes "Little Jewel" chassis, and got the power supply and PP output section completed, but then the move from NH to NC got in the way, and now it is sitting inside one of many yet to be unpacked boxes in the cellar, two years later
For the input stage, a 12AY7 isn't absolutely necessary, it works very well with 12AX7 or 5751. The three different tubes will give you slightly differeing tonal qualities, so it ends up being a matter of personal taste. The 12AY7 has the lowest gain (40) , the 5751 is in-between (70) and the 12AX7, the highest gain (100).
/ed B