This is my daughter's 05 GT...im not sure what all has been added to the engine as she bought it from a coworkers boyfriend so any input would be appreciated as we need to verify what needs to be fixed...she said the timing belt broke and I believe it threw a rod

 

1, the little air filter where the oil goes shouldn't be there. 2, there are adjustable struts up front, probably matching ones in the rear. 3, the 05' to10' 4.6 3V doesn't have a timing belt, it has 2 timing chains. the stock intake looks like it was just put back on, the car likely has a tune on it and it runs like garbage I would assume since the stock air box is on it. where did you get the car? how many miles? auto/manual? give us as much info/pics on the car as you can. clean all those pine needles from the cowl, then remove the cowl and clean the channel out, then look how to clean the firewall drain plugs. id bet that the passenger side floor has been soaked more than once and the SJB has been compromised. peel back the carpet and check for water damage.

 

As previously mentioned, the 4.6 3V has a timing chain to each camshaft so there's no belt. It's possible a timing chain guide broke on the old engine causing the chain to jump a few teeth. That would have caused catastrophic engine damage so the car probably has a junkyard replacement engine.
The engine looks bone stock apart from a Ford Racing passenger side valve cover breather, which shouldn't even be there 'cause it's causing a large vacuum leak and an oily mess. You'll need to replace it with an OEM oil filler cap.
It looks like the positive battery cable to the starter and the B+ cable from the alternator have recently been replaced, perhaps at the same time as the engine.
The car desperately needs a thorough cleaning and some love. It's obviously been parked under a tree and the cowl drains could be blocked. The previous poster has given good advice about what to do about it.

 

Yep, looks like it has been parked under a Georgia pine tree