65 Dart Wiring Harness in a 66 Dart

one of the 3 years had a different bulkhead connector (3 maybe) 66 was different.

63 and 65’s used a solid buss bar through the bulkhead connector for the battery and alternator wiring rather than the Packard 56 terminals, IMHO a much better solution.

#1 Aside from the obvious instrument panel difference 65 round, 66 retangular, which I can modify, are the harnesses the same?

With the buss bar arrangements, definitely not the same. Location of other terminals within each bulkhead connector are probably different.

#2 Can I replace the old style Fuse Box with a new universal blade style. I plan on eliminating the Bulkhead connector too. Wire it straight through the firewall.

I don’t see why not. In my 65 Dart My underdash harness is basically a marriage of a modified 65 Dart bulkhead connector with 3 buss bars to a modified J Body harness to aftermarket blade fuse panel(s). My engine harness is basically a modified 65 Dart with headlight relays and maxifuses protecting the alternator wiring and wiring going inside to the ignition switch and headlight switch