First Check out John B's web site. It will answer a lot of your questions.
http://home.earthlink.net/~bzdel/ John sells the Engine Mounts for the Swap, modifies the F-Body Oil Pan and sells an Air Condition Compressor relocation kit. Nice guy to deal with.
There are several guys running truck motors on here, so hopefully some of them can give you better answers with regards to using the truck accessories, I believe the altnerator is too high to clear the hood, but someone may have found ways around it.
The F-Body accessories work well with the John B mounts except that you have to move the air conditioning compressor. I just dropped my motor in with John's mounts and everything seems to fit well.
I am pretty sure the F-Body Exhaust manifolds will work. (I will have a set of 2000's to sell once I am sure my headers will work if you are interested)
I am not sure about the trans adapter, might be better off just trading your BOP pattern trans for one with the Chevy pattern. Some 200r4's are dual bolt pattern so check yours before invest in a new one.
Some guys modify their own stock harness. Speartech is the place that everyone seems to recommend for modifying harnesses and reprogramming PCMs. The owner is a regular here. If you call them they can explain the VATS, etc. But you will need some reprogramming.
I have not gotten to the steering box yet, but you can connect the 5.3 pump to the stock steering box. I believe you have to change the lines or use some adapters as the fittings are different. John B's website walks through what you need to do here.
Pan Choices are F-Body, Truck or aftermarket. Most say the truck pan is too deep and will have ground clearance issues. A lot will have to do with your ride height. Some guys run the stock truck pan. I think some modify it to shorten it. The F-body generally needs to be modified slightly to clear the cross member. (Some people also notch the cross member). I am not sure about the aftermarket ones. My concern with them is that the Oil Pan is supposed to be structrual on the LSX engines. The factory pans are pretty thick cast units. I am not sure how good the aftermarkets ones are.
Bottom line is that there are a lot of options and not all will work well together. Best thing to do is go through the couple of G-Body Threads here and look for the guys who have 5.3 and 6.0 Truck motors and PM them to see what they combination they used and see which one works best for you. You will find people are really helpful here.
I will shut up now and let the experts correct me!