What ever happened with the chrome plated master cylinder rebuild? From what I have been able to tell from looking at your prior posts, the system has never worked right? Can you summerize what was done and what where the results after?
It looks like you have done some solid work and also, your home work. I am assuming that the pads of been bedded:
http://brakepads.wilwood.com/03-tech/index.html
That you have your balance bar set up correctly:
http://www.tiltonracing.com/ins/98-1250.pdf
The MC pistons are allowed to fully return, the balance par is perpendicular to the MC pushrods when the pedal is fully depressed and the bar does not bind at any point during travel correct?
I sounds like you bled them correctly (you where careful not to open the bleeders to much right?).
One of the big variables I don't have for your car is the CG height. If you care to measure it, I would really like that!
http://www.longacreracing.com/articles/art.asp?ARTID=22
If you master cylinder reserviors are remote, they are mounted above the master cylinders with no point of the line connecting the two below the MC correct?
Did you put in residual pressure valve and if so, what psi rating?
This may sound like a strange one but it helps know what kind of pedal pressure is acceptable for you. How is the leg? Seats overstuffed? Try placing a small bath scale on your pedal and press as hard as you think is reasonable, what does the scale say?
The brake pedal does not overcenter does it? That is it does not travel past perpendicular to the line of force (hip to pedal) does it?
Have you properly adjusted your bias? Probably impossible at this point I understand.
Do you have access to a set of brake pressure guages. Hard data is a wonderful thing.
Back to your problem. Considering what I have read, I would say that the problem is related to one of the set up items above (such as balance bar and pushrod adjustment, reservoirs, bedding, the plated MC's, etc.). I would go through the process of elimination on these first.
As far as master cylinder size....... EM seems to think the CG is below ground, Tilton about the height of an SUV and Wilwood some where in between. The varied pedal issue of course has nothing to do with the MC size, although after all those cylinders have been through, it still could be them!
Try the CG height on the spreadsheet I sent you and watch what it does to the graph, makes a big difference doesn't it? Basically what you are trying to do with that spreadsheet is to line up front and rear brake pressures with the front and rear pressures for the master cylinder given for the desired rate of deceleration and pedal effort. Study that chart and vary the master cylinder sizes and you will see what I mean.
If you look at the spreadsheet I sent you, notice how the front and rear master cylinders are the same and that they line up fairly well for a .5g stop with just under 50 pounds of pedal pressure. Count over to .9 g's (fifth red and blue line from the left) and notice how much more front pressure you need. At this rate of braking, you have entirely to much rear bias. Now, play with the balance bar. Change cell I18 to 1.1 and notice how nicely that between 40 and 50 pounds lines up with the .9g stop.
This can not replace real world testing, but it does let you play with the vairables before you spend the time and money chasing parts. Let me know if you have any questions.