I have a 1995 ford f150 I bought that had been sitting a couple of years, the battery was dead when I bought it. After I bought it I put a battery in it I noticed that when I open the drivers door the theft light flashes, if I turn the key to on the engine will not turn over and the theft light stays on, if I shift the truck into neutral and turn the key the starter activates but the motor will not start, I'm trying to figure out if it's because the theft system is interrupting the ignition or if it's cause of an issue with the motor or bad just bad gas or other engine problems.

I don't want to go through the trouble of replacing the engine only to find out the new motor will not start either because of a anti-theft system, is there a way to bypass or disable this theft system for example by disconnecting it or splicing wires together somewhere?
I did check all the fuses and none were blown.

Btw, this is what the truck looks like:
longisland.craigslist.org/cto/3242683319.html

 

Assuming you have a factory installed alarm try this:

Disarming a Triggered System

Performing either of the following steps will disarm the triggered alarm system.

1. Driver or RH front door is unlocked with a key.

2. Driver's door is unlocked by pressing the UNLOCK button of a remote entry transmitter.

Two minutes and 45 seconds after the system has been triggered, the horns and exterior lamps will shut off automatically. The system will then reset to an armed state and will trigger again if another intrusion occurs. The vehicle's starter circuit will remain disabled until the system is disarmed.

 

I had a supercoupe that had factory theft.
I got around the alarm and no start by...

Unhook battery
Turn key to run
Hook up battery
Start car

Worked every time.
Search eBay for a remote for your truck. It has only cost me 10-14$ per remote
You can activate them yourself usually.