timing gear alignment.

Explain!

I don't see how it can be any other way.

The crank gear can only go on one way.

The cam gear can only go on one way.

With the dots aligned per the FSM you are good to go.

(Timing the distributer is a separate matter)

If you set the crank to have the #6 ( your words) cylinder at tdc then that would make the dot at 12:00. There is no other position that the dot is at 12:00 on the crank.

Same holds true for the cam. There is only 1 position that the cam gear dot will be pointing to 6:00 and I assume based on your statement that #6 is that position, then the cam will be on the #6 compression stroke.

I have explained in both my previous posts. Let's see if I can do it again. You're assembling a new engine. Let's say since the OP's engine is a slant 6, that's what we have. You align the crank and cam sprockets with the marks facing each other. Cam sprocket dot at about 5 o'clock and crank sprocket at about 10 o'clock. Dots aligned. With me so far? Now you continue on assembling. Put the distributor in pointing to number 1. Right? WRONG! Because when you time dot to dot at the cam and crank you're timed on #6, not #1. Understand?