1997 cobra motor finally toast after 180,000 miles

What's up everybody!

I have a 1997 Cobra that started to make a weird knocking noise first when I would take it up to 3000 RPM and then eventually at every RPM, then shortly after it would either die while sitting at lights or at low idle. In the days before, I noticed it would crank for a while before finally getting started; didn't know if this had anything to do with any problems. Strangely enough, I also had a hot wire short somewhere in the car around exactly the same time! The same day that the Cobra died, I looked under the hood and saw that both of my terminals were melted clean off the battery. I went to get some new terminals and installed them no problem, and was able to start the car back up. I then put a stethoscope to the passenger-side valve cover to discover the source of the knocking sound. I wanted to determine that since it wouldn't start, perhaps it was the fuel pump malfunctioning or perhaps some detonation occurring as a results, or just a plain old rod knock or bearing issue. I went to remove the valve cover and couldn't get it off all of the way because the fuel lines were in the way just about where they attach to the fuel rail. Obviously I would have to relieve the pressure using the schrader valve so that I could disconnect the fuel lines, but I realize the engine had 180,000 miles and it wouldn't make much sense to fix the internal issues and get it back on the road with the rest of the internals in their current state.

I am considering buying a motor to put in, preferably something like an LS crate motor if possible or another 4.6 4v Cobra engine. My cost is about $3000, what should I do? What would you guys do? Is it even worth diagnosing my issue and using the same engine? I love my car and don't want to sell it but I want to get it running again with either a rebuilt motor or completely new motor. Thanks!
 
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