Auto NA miata main wiring harness question
 

I have a 1994 auto miata that I got as a roller and I started collecting parts for a 5.0 5 speed swap. I started working on the car getting it ready for the swap. I pulled the dash out and found the the PO cut through the main harness in two spots. I found a local guy parting out a 97 auto and he gave me a great deal on the entire harness. I have the harness installed and I installed all three pedals from a manual 96 miata.

Before I bolt the dash back in I had a few questions.

I removed the flasher relay from the auto bracket that has the resistor and installed that but left the other relay and resistor part out, is that ok?
Do I have to cut or jumper wires under the dash in the main harness to get the speedometer to work? I read a post that this needed to be done but I dont understand why.
How do I wire the neutral safety switch?
Any other harness modifications I need to do before the dash goes back in?