We need a bit of clarification here, are we talking 325v/380v AC or dc? Loaded or unloaded?
Tone Clone is a brand name, not a mission statement, MM offer a whole bunch of options, they can't all be right.
A Tweed deluxe (or clone) might run 350-385vdc after the rectifier (NOS 5Y3) BUT unless MM knew what rectifier you were using they wouldn't know this and I doubt they would include it as a a spec for a PT. Confirm with them what dc voltage you should see after a NOS 5Y3. 380-0-380VAC rated secondary B+ winding will NEVER give you 5E3 type voltages. 330-0-330VAC B+ secondary will be about right.
The Sovtek 5Y3 isn't really a 5Y3, if you really want to use a 5Y3 buy NOS, or maybe try a 5V4, these are very popular for 5E3.
Your heaters will measure 3.15VAC from each leg to ground, really you want to measure from pin 2 of a 6V6 to pin 7, you should see >6.3VAC.
Centre taps from B+ & 6.3VAC heater windings should be grounded, there is not usually a centre tap for the 5VAC rectifier winding (though Hammonds have them). Confirm?