The engine still should run with the brown wire disconnected. The initial timing should be enough to at least let the motor idle. Whatever the label says to set the timing, say 4-degrees before TDC, with the brown wire disconnected, should set the MIL light and a code in the ECM, so you'll have to clear both after you're done with the timing.
Did you have any codes stored in the ECM after the motor started to exhibit the stumble? OBD ll vehicles are usually (but not always) easier to diagnose because of the codes they throw. It might pay to have someone hook a scanner to it, if you haven't done so already. I had a neighbor who's Firebird had a terrible stumble off idle, hooked the scanner up and found the ignition system wasn't advancing the timing at all! No hair pulling necessary!
Just a few ideas...............
Lew