troubleshooting - wont start

Hello everyone, my first post here. As of this past Sunday I am the new owner of a 1996 4 runner. The body is in really good shape, the interior not so much but its manageable. So the important part, the engine.. where my current problem is. So let me explain, the vehicle has 280,000 miles on it. I bought it from the second owner of the vehicle, he put the large majority of miles on it. They were mostly rough on the interior with animals, smoking etc.
Engine wise, the guy changed fluids often. I dont see anything crazy, just a ziptie holding a clip on, little stuff.. 98% of the engine & its components are intact. He had surgeries & gotten down, so the vehicle sat up for about 8 months, hasnt been drove in almost a year. Before that he drove it regular, never ran hot, the AC works!
When I picked it up, I could crank it, rev it to about 1700 rpm & it would stay running. You could even put it in gear & drive it, it just ran rough.. old gas. By the way -- I gave $1400 for it, it had been out by the road for an hour. So that is the back history. Now I have this problem...
I trailered it home & was tinkering with it Monday after work & I depleted the battery. I could not move it closer to the outlet so I took the battery out to charge it over night. I put the battery back in & when connected the vehicle makes a loud pulsing beep (not the key beeping or blinker) sounds like a security noise & some lights are flashing with the beep too, & it will not start or crank. All my accessories are working, battery is good, & it was cranking up before..
So is it in security lock, do these models even have a security lock??
Its going to a mechanic soon to completely check it over, at least get it driveable I can go from there. My wife & I just had a son, so my hands are tied sometimes ..it will be a great vehicle for him when he is 16 though.
I did find a good parts 4runner that I will have to drive three hours to salvage the seats & anything else, if there is anything important I need to get off that thing you guys let me know.. this is my first Toyota I am loving it, even though its sitting out there dead lol.
Help me get it back started, at least I can drive it on/off the trailer. Thanks!!