Based on the layout and chassis pictures I have seen, you most likely need the longer style fuse.  But just why did the fuse blow in the first place?  By using the higher wattage fuse from the DR, you risk damage to the amp.  I would explore that avenue unless you know why it went in the first place.

Don't know if you fixed your problem yet but you most certainly need to ground the center tap of the power transformer!  The center tap of the heater leads should also be grounded (you will have a lot of hum if not) but that would not cause the PT to smoke- the HV center tap not being grounded will!  I hate to tell you but you most likely burned up the unit.
   Don't think me too critical but should you really be messing around inside an amp?  This is basic stuff you have got to know before you go into the chassis.  Don't want to come off sounding negative but you can really hurt yourself and damage the amp.

Hi- I have built this great sounding amp and been playing it quite a bit.  One thing I don't really care for is the need to have an A/B box and 3 cords to do the psuedo channel switching available.  Just too many cords on an already crowded floor setup.  So, why not install one of those nifty little channel switching kits like I see at Skip's circuits or similar?   If you look at what's going on in the amp, its really just two separated input jacks feeding two separate circuits that meet up at the phase inverter.  So is there really anything more involved than a simple common input jack feeding a relay driven switch that can be actuated by a simple mono foot switch?  One part of the relay direct the input to the low gain and the other part directs it to the high gain.  Am I missing anything?
   Has anyone done this?