> it looks like the stock valve jr has a 12V secondary
Looks like 6V to me. Powers the EL84 directly. When rectified onto a big cap. we get ~5.9VDC.
But you can't power most 5V rectifiers from that winding, if it is feeding your 12AX7 and EL84 tube heaters. The filament of most 5V rectifiers sits at the B+ voltage, ~+360V; the heaters of the 12AX7 and EL84 have to sit near their cathode voltages, essentially zero volts, or within about 100V of that.
You can try to find a heater-cathode rectifier with 400V of heater insulation and maybe 40mA current capacity. 6X4 will work (except the Epi's HV winding is wrong for a common-cathode rectifier; see below).
But I really think: you add another big bottle, you need to add heater power supply. If you are not going to replace the original main transformer, you will need an extra trannie just for the wrectifier. 5V at whatever current is ideal. A 6V winding may be easier to source: use Ohm's Law to figure a resistor to drop 1.3V at the rectifier's rated heater current.
Note that the 5V4's heater alone eats more power than the 12AX7 and EL84 heaters combined.
And you KNOW, for ~~$99, Epi didn't build any excess power capacity into that amplifier.
> output transformer for this amp that will have a 4,8,16 outputs?
The Head version has 4 8 16 taps.
> Can I use the 260V secondary safely?
That is a single winding, suitable for a Bridge (4 diode) rectifier. The 5V4, and most bottled rectifiers, are 2-diode with common cathode. What they really want is a center-tapped winding. Using the Jr's single winding, the only pure-bottle way to go is a Half Wave rectifier. Half of a 5V4 is plenty big for this ampifier, and the ~320VDC is fine, but the buzz will be bad and the power transformer will be unhappy about the half-wave load.