X Head Assembly & Installation - Comments Requested

As some of you know, I am in the process of a minor rebuild of my 340. The project has turned into something way more than my capabilities but with the help here I have managed to get to the final assembly stage.

I originally thought I had a head gasket leak so I removed my x heads and had them cleaned and checked by my local machine shop. They came back with A+ marks, flat as can be and no cracks.

The heads have the valves still in place but the rockers removed. They were nice enough to tie off the ends of the rocker shaft so all the rockers are in their original place.

I am going to check the block for flatness prior to installing the heads.

I will also check the gasket to the head to ensure no passages are being blocked. Then I am going to place the gasket on the block and then the head.

My first question: The FSM says to coat the gaskets with a sealer. Is this necessary? If so, can I use Permatex Gasket Sealer? I have this already.

Second question: The FSM states 95 ft-lbs as the final torque spec. Is this correct? I know some things were misprinted in the FSM. I understand the torque sequence.

Third question: Are the heads "driver" and "passenger" ? Or does it not matter?

Forth question: I am using a thinner gasket to pump up the compression a little. The new gasket will be about .02 to .03 thinner. Will this force me to make adjustments to the push rods, arms or valves?