Pulled the Mess that was my Timing Chain....

Don't even worry about the dots for ign timing. Put number one cyl at TDC compression (both valves closed) install the distributor with the rotor pointing at # 1 spark plug tower.
Turn dist so the points just open (if using points dist), or the reluctor is even with the pole piece of the pickup (electronic dist).

FYI: if you have the dots lined up, #6 cyl is TDC compression, and if you install the dist pointing at #1, your timing will be 180 degree off.

PS: Where has your shop instructor been during all this? Hasn't he/she been able to answer most of your questions?