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.