I presume the wires you are referring to are in the stock wiring harness......right? If so (according to the wiring diagram) the brown wire is the Tach wire that would attach to the (-) negative terminal on the coil and the other wire should be the white/orange/purple that would attach to the (+) positive terminal on the coil and the yellow wire would also be attached to the (+) positive terminal on the coil. These wires would have been disconnected upon installation of the 6A and the new wires from the 6A would have been connected to the coil, distributor, and tach as follows.....
Orange wire to the (+) positive terminal on the coil
Small Black wire to the (-) negative terminal on the coil
White wire connected to the original distributor wire
Gray wire connected to the original brown tach wire
Smaller Red wire to the ignition key
Large Red wire to the (+) on battery
Large Black wire to the (-) on battery
Those wires that were removed and not re-used at the original wiring harness should have been taped, folded back and tied down to the original harness.
Hope this is what you are looking for.
BTW.....here is a link for the MSD installation instructions......
http://www.americanmuscle.com/msd-6a-digital-ignition-7995-install.html