I'm not the best guy to be helping you with this, but here it goes.  For me, or anybody else including you, it is important to know which one of your transformers "blew" and why.  Off the top of my head I would say you have a bad power tube.  But you could also be looking at a bad PT, filter cap, or even diodes in the rectifier circuit.  Are you sure you have a "Slow Blow" fuse for the HT ?  Do you know how to build a light bulb limiter?  Do you have a copy of Gerald Weber's book?  He has a pretty good routine for checking fuse problems.

Hey Gerry -
Just want to make sure I understand you correctly.  Are you using some kind of star ground/ground buss that ties EVERYTHING to ground at either the PT or the filter cap?  If that is true then you are fine the way you are.  IMO it is best to not have any redundant ground.  I think it works out good for you that the chassis IS painted.  As you say, just scrape off the paint at your two ground points and you are done.
If, of course, you were planning to ground the pots and jacks via the chassis, then you have a problem.  But something tells me you have it all figured out to perfection. 

I am not sure if anybody makes a real 5881 anymore, other than TungSol.  I think that is why you are told to use some variant of a 6L6.  I would maybe ask Nik his opinion.  But also ask one of the tube guys:
Doug at Doug's Tubes
             or
Mike at KCA NOS Tubes
Either one of those guys can set you straight.
Good Luck

So you are seeing a difference of 6 milli amps between the two tubes.  That is nothing to worry about, just means that your tubes are not matched real close.  I would just set bias by the higher reading of 40 MA.  So you are right at about the 70% mark now.  I would say you are just about perfect where you are. 
It does seem that something is not right with your Presence control, but it is so hard to READ about what other people HEAR.  The other pots should also be giving you noticeable adjustment.  I do not really know how to respond to that.  Maybe some of the other guys will have a suggestion for you.  Are you the original owner of this amp?  Or has somebody been inside of it before you?

I am not sure what the Weber "method" is, but 36-40 MA is what most people would say is just about right.  Do you have a DMM?  Nik installs a 1 ohm resistor in his amps... cathode to ground.  It would be interesting to see what numbers you get there.  Just set your DMM to VDC and take a reading from ground to pin 8.  It will be a direct conversion to milli amps,  .038 would be read as 38 milli amps.  Needless to say, you take this reading without your Weber installed.
If you do not have a DMM... well never mind then.

To prove or disprove that, we would have had to buy two sets of caps at the same time and assume they were all made from the same run of materials.  Then you would have to put 100 hours on the one set of caps, then install both sets into our two similar amps.  That is something we did not do, so I really can not give an opinion.  I have a hard time accepting a "break in" period for caps, but I am sure there are knowledgeable people that will defend the theory.  Personally speaking, capacitor break in time is something I will never worry about.
Good Luck

We bought two identical 50 watt leads over a year ago, both with MV.  It really gave us the chance to do a lot of comparing.  The first change I made to one of the heads was to get rid of the Mallory 150 caps and install the "basic model" Sozo's.  With just that change alone, yes you could hear and feel a difference between the two heads.  We had quite a few players (I believe it was 5 guitarists)  test drive the heads for us side by side.  Nobody was told which head had the Sozo caps installed.  We just told the guys that we had made a change to one of the heads.  Four of the Five players said they preferred the head with the Sozo caps.  Nobody said either head sounded "bad", just that they definitely preferred one over the other for tone and feel.  Because I knew which head had the Sozo's, my opinion is biased, but I preferred the head with the Mallory caps. 
So that is my experience.  If I had to make a definitive statement I would say, "You will hear and feel a picking difference with a change to Sozo caps, but it is impossible to say if you will think the Sozo sound is "better" or not". 

What kind of numbers do you see for plate voltage and plate current?

Hey Mark -
I do read TAG sometimes.  But if i seem familiar to you it is probably because you have helped me out here before.  I guess if I were to use the speaker jack as the NFB source, I would be increasing or decreasing the voltage to the NFB resistor any time I went to 4 or 16 ohms?  I assume at 8 ohms the NFB would be functioning as designed?  But to answer your question... no.
I should have been a little more forthcoming with my original post.  I was having a lot of feedback and oscillation troubles with this amp.  It took quite a bit of fooling around with lead dress and component changes to tame the troubles.  It seems that I now have the amp pretty stable, for a TrainWreck type of amp.  I can imagine what Ken Fischer must have gone through.  Amazing he did not give up at some point.  I realize he had much more ability/knowledge with electronics than I do, but he had no guide with him.  I see the PI looks like a "Plexi" but I imagine the rest of the amp was mostly KF tinkering with his ideas.  Anyway.......
Thanks for your help again.

Nice purchase, I think.  Not a huge Marshall snob, so I do not know all their numbers.  This is the Silver Jub I assume.  Will be nice to hear your opinion of the amp and also some sound clips for sure.  Have you decided on a cabinet/speakers yet?
And we will be expecting several pictures also. Do not come back here without pictures.

If you bought your tubes from a decent dealer (Doug's, Tube Store, KCA, Euro Tubes, etc.) they will already have been "burned in".  I do not know where Nik gets his tubes from.  Generally the dealer will install a box of tubes in a burn box that has a lot of tube sockets to accommodate all the tubes.  I think 48 hours is the standard time period.  It is basically a pas/fail test because modern day tubes can have a pretty high rate of failure, even right from the factory.  Other than that I would not worry about it.  I would not want to gig with an amp full of brand new tubes, but just install them and play at home for awhile.
Good Luck

M Fowler,
Thanks for the help.  I finished with a 51k resistor at the NFB position.  I also played around with the lead dress a little.  I separated the plate load wires that were tied to the NFB wire which helped a bit at volume.
Thanks Again

I know the value Nik uses for the NFB is 100K.  But what value resistor are you guys ending up with for the NFB?
Thank You

Well, we were having oscillation problems so I started making changes.  I did go with a 12AT7 for the PI, there is till plenty of wildness left in the amp.  It all depends on the player and the guitar.  It is so easy to change pre tubes; all I can say is try it yourself and see what kind of results you get.
Good Luck

Did you try a new rectifier tube?