I do have access to the car, but don't really have the space/tools/equipment necessary to pull it apart over the winter. My thought is to get it looked at in April as soon as I can get it on the road. Right now I'm thinking I will take it to Steele and ask Art to work on it as I don't really know anyone else that I would ask to do engine work. My dilemma is, what else should I upgrade at the same time.....

As for the crank shaft end play, what you describe is what Art described, but not sure how to check it with the motor in the car..

Not sure if it can be done in car or not. Normally it is done with a dial indicator on the end of the crank shaft so it measures front to back motion. Then pry the crankshaft all the way back, then pry all the way forward . The difference as measured with the dial indicator is the end play. The trick is where to pry from. Normally the pry bar would be on the block somewhere.
No sure what the spec is on end play, some one may hoist in with that.

This method over many years and recommend that you do not assume the trouble is a certain part, as a problem in one area will often show up as a symptom somewhere else. An example is carb malfunctions are often incorrectly assumed to be governor problems.

Spec for the crankshaft endplay 2001 mustang GT 4.6 sohc is 0.003-0.015", but you are right that it will be hard to check with the engine in the vehicle. Noise could be coming from a lifter, stretched timing chain, or any number of engine components, so pin pointing the noise is a must before disassembly and measuring all components and comparing to specs.