tito911s,
The nuts and washers being magnetic is a non-starter. As far as I know, all head stud nuts are steel. Measure the stud height on each bank (1-3) versus (4-6). You'll probably find the bank that had the washers will show higher stud height. I would not abandon the 964 nuts, many builders on this site have recommended them.
I have 993 turbo head studs on my 3.3l turbo and even though the threads were cleaned with a thread chaser, not thread tap, the stud height exceeded 135mm by a couple of millimeters. The 964 nuts gave me the margin I needed to insure proper torquing and clamping force.

I agree with Chris, use a nut and washer and not worry about stud length and the idiotic tool engagement depth. You already have non stock studs so a non stock nut will match just fine.

Of course, since the prior assembly method was fubar'd, I would pull the studs and sanity check that the stud installation job was done correctly. I could not live with that nagging doubt.