Truck Intermittently Will Not Start

So about a month or so ago I broke the truck something bad. One of the parts to break was the transmission. I had it replaced by a shop with a Jasper unit but that is when a new problem started that I never had before they touched the truck. As soon as I got the keys back the truck would not start, dash lights up and everything but then would only click once but starter would not crank. The click sounded like the three or so clicks you get with a dead battery but only one click. The issue occurs randomly so it is hard to tell what is wrong, I was thinking starter and when it wouldn't start one day I tested this by hitting the starter then it worked and thought that told me that was the issue so I replaced it. What I think really happened was I pulled the key and put it back in because that seems to usually get it to start. The new starter has a skreetching sound at the end almost like its sticking, wish I didn't replace the starter but that is for another time. After not starting the truck for a little over a week the start was slow and long but started first try. So my other thoughts are the battery being a little dead from something draining it, starter relay, transponder key amplifier, ignition lock cylinder, ignition starter switch, or key inter lock solenoid. I am leaning more towards the relay or amplifier because the viper remote start does not work anymore either, the dash lights up you can hear a click in the engine bay then like power is going to something but not a full click. I know this is all hard to explain I can try and get some videos but that is hard to do since it doesn't happen all the time. Any thoughts or tests I can do to figure out what the issue is?

EDIT: Forgot to ask if there is some form of neutral safety switch or something on these trucks. Although the truck is not throwing any codes that I can tell.

 

What’s the battery voltage when off?

 

If all these problems started when you got the truck back from the shop why didn’t you take it back and have them fix it.

 

Viper Remote Start?
I think you have found the problem.

 

I will have to check that maybe when I have a starting problem and when I dont?

I was in the process of moving and had no time plus it kinda stopped having issues for a little while so thought it was a fluke due to the new trans.

The viper system has been in the truck for about 3 years now no problems whatsoever.