I don't have the technical knowledge to comment on making a change in the PT and the choke. I think it will change how the amp sounds, but can't say how.
For the VA rating, this is rather simple. You will need a tube reference to look up how many mA each tube requires. You can download the TDSL from Duncan:
http://www.duncanamps.com/tdslpe/
You'll see that a pair of EL84 needs 72-92mA. A 12AX7 needs ~3-4mA.
(2*92mA) + (4*4mA) = 184+16 = 200mA. That's your 200mA for the high voltage secondary. Add a little something if you want a cushion, but it should be fine at 200mA.
Assuming about 300V @200mA = 60W. Adjust as appropriate, but 300V for EL84's is probably upper end of the relevant range.
Next, add what's needed to support the filament winding. EL84's need .76A each and 12AX7's need .3A each. (4*.76) + 4*.3) = 3.04 + 1.2 = 4.24A. 4.24A * 6.3V = ~27W. If you also have a 5V winding or a second 6.3V winding, include that as well.
27W +60W = 97W. Let's round to 100W for discussion. Allow for some power to be lost as heat. Amps are not all that efficient. I'm not an engineer, so I am unsure of the proper de-rating factor here. I was thinking a push-pull amp is about 75% efficient and you need ~150VA on the primary. A single ended amp is only about 25% efficient, so, if you are doing this for SE, de-rate appropriately.
If you take the MM data and add it up:
355V *200mA = 67
6.7V * 6A = 40
27 * 1.5A = 41
67+40+41 = 148VA. I believe the 6.7V winding is generously sized, which allows for less of a de-rating factor. 150VA seems perfectly reasonable.
I hope this makes sense. Your transformer winder should be able to do this with his eyes closed.