So basically took the valves off, took the coil wire off, adjusted valves (the coil did spark while doing the valve adjustment). Put on new gaskets and valve covers all tightly sealed, nice and neat, GM performance valve covers and everything:D.

Buuuut...car doesn't start now. It did run yesterday just to be clear. Mechanic came over and was helping me go through it, pulled the MSD box and the LED light is blinking red 3 times, pausing, blinking red 3 times again. I can't find exactly what this indicates and the MSD website doesn't tell me exactly what this means. Anyone got any ideas?

My mechanic followed the manual for the 6AL2 (here it is http://msdignition.com/instructions/Products/Ignitions/6421.pdf?terms=6421 ) and looking at page 9 created the short and got a successful spark from the coil. Buttttt the engine still does not start. Whats going on?:confused:

I would check the dist cap and rotor. I went to a cruise once and my car would not start. I did the test on the msd box and had spark to the coil wire. Still would not start. Pulled the cap off and the tip of the rotor was broken and turned side ways.

But I have the MSD 6AL.

Sounds like you spiked the box..