Are you talking about the accordion hose which is rubber and connects to the turbo or the hard plastic which holds the air filter and bolts to the afm? If you're talking about the accordion hose you can get one brand new on driftmotion.com for a pretty fair price otherwise watch the FS threads for a good shape one.
The tranny cooler lines are bolted to the engine in 3 different places iirc. If you're pulling the engine too I would just leave them attached and disconnect them at the tranny and pull the whole engine and tranny as one with the lines still attached just be careful that you don't bend them.
As for the exhaust nuts, they are studs with nuts on them. I doubt they'll break off, if anything you might just pull the whole stud out of the elbow. If they do break then you get to have a ton of fun with a drill and get some cobalt drill bits and drill them out big enough so you can retap them stock size if you can.
You should be able to reuse the torque convertor they usually don't go bad that often.
To get the engine out you will have to atleast take off the upper intake plenum. so you can just leave all those metal lines under there just make sure you get the fuel lines disconnected and all the connectors under there. The starter wires are usually kind of a bitch but with some patience and good hands you can get it.
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