No theres nothing different between the MSD & stock distributer,when it comes to dropping the distributer in the block.If you wanna double check the distributer to make sure its installed correctly,do the following:
1) pull the #1 spark plug & stuff a piece of toilet tissue into the plug hole slightly
2) use Witeout to draw a line over the 0° & 10° btdc mark on the balancer.This helps you see the marks easier with the timing light
3) use a torque wrench/breaker bar & socket to rotate the crank CW until the tissue blows out
4) continue rotating the crank then stop once the 0° mark is aligned with the timing pointer
5) remove the distributer cap & look at the rotors position
6) it should be pointing straight ahead,between the front two upper intake bolts,like shown in the picture below
7) if its pointed correctly,start the engine and let it idle until it warms up,barely loosen the distributer holddown bolt,remove the spout plug,aim a timing light at the balancer then rotate the distributer til the 10° balancer mark is aligned with the timing pointer,tighten the bolt,plug the spout back in.
8) if its not pointed correctly,pull the distributer,rotate the shaft slightly then drop the distributer in until it is pointing in the right direction.Once its dropped in correctly,follow step 7 to adjust timing to 10°
9) once its set to 10° & the spout is plugged in,aim the timing light at the balancer again to make sure the ecm is advancing timing properly.
Timing should stay at a fixed position with the spout plug removed & a advanced/fluctuating position with the spout plug installed.If you see the timing mark bouncing back & forth with the spout plug removed,the balancer ring could be bad or the spout wires could be shorted in the harness.
Make sure youre on the compression stroke too,not the exhaust stroke,when you drop the distributer in the block.If its on the exhaust stroke,it will possibly still run,but it'll run like crap because being on the exhaust stroke puts timing out 180°.
Triple check your plug wire routing on the cap too.The distributer cap adapter has two metal clips that holds the cap on.The #1 plug wire post is two posts to the right of the clip on the left side of the cap.The firing order is 13726548 CCW.
You can also run a cylinder balance test to see if the ecm id's any specific cylinder(s) as having an issue.The procedure is listed below.Once you click the link,scroll down to the appropriate section.
DIY KOEO/KOER/Cylinder Balance Self-Test Procedure