I have not driven the ZF, but I like my 4500. From searches I did back when, the 4500 was supposed to shift a bit smoother. It does have a little bit of a long throw, but its not as bad as the 3-on-the-tree. If you get one of the newer style 4500s with the rectangular shifter mount (as opposed to the socket-ball-style) then I believe there are short throw shifter kits out there for those. You can replace the shift tower to the later style, but the newer bolt-on-shifters style towers are in demand and more $ and I didnt want to spend the extra $.
You can buy the NV4500 install kit for about the same price as a NV3550 kit (~$800 +/_) or a ZF kit. The mount from AA is not included with the NV4500 kit, like it is in the NV3550 kit (even though it apperas to be the same mount)...but it will only cost you $100 from AA. However, it might be easy enough to fab your own for less, but I didnt want to mess with it for only another $100. Then the big price difference only comes down to the tranny itself. You can find deals on NV4500s. However, but b/c they are more desired by multiple vehicle swappers (jeeps, Toyotas, Dodges, Chevys--most swappers actually), they usually have a small premium over a ZF--which is mostly desirable by us Ford folk. Without a core, you are looking @ ~ $1900-2100 or more. With a core a complete rebuild with new counter and mainshaft should be between $1K - 1.3K depending on the condition of the gears....less if you have friends. The cost to rebuild a ZF should be about the same...either way, if you can find a "core" which can be hard, especially for the NV4500s, thecost to rebuild is comparable.
I think WH charges more, b/c they also include a new steel tunnel piece, the tranny mount and such.
With the $800 kit, the $100 crossmember, you are just looking for a quality rebuilt unit...and of course a new clutch as you would install with any new tranny...I am not sure why some of the 'all-included' kits warrant the $3-3.5K pricetag. I would NEVER install a tranny that has not been at least inspected, better yet, rebuilt by a qualified and competent shop. I got burned by an individual named Jim Clark (who I had used before and recommended to others) with an inferior 4500 tranny for my frame up--likely was not even rebuilt. He promised me he would make it right, but moved, doesnt return calls, etc. I gave up on him. Another friend of mine is also dealing with a leaky 4500 from him. After 1st gear went out at 10K miles, I had a real shop go through it...thats where I get the $1-1.2K rebuild price from....so my "really good deal" turned out to be a "install it twice cause its fun-- and, hey, you spent the same amount overall as a brand new kit deal anyway-deal". Actually, I just installed it a 3rd time, b/c the other shop that rebuilt it didnt get it sealed well enough...so they went back through it again for free...but I still had to remove/install it again. At least they stood behind their work. Did I mention that I could do one of these swaps in my sleep??....I've done the 3550 install 3-4 times now as well (for myself and then helping a buddy).
I know I am long-winded, and for that I apologize, but I have to say it again....QUALITY PARTS...make sure you install them...doing things more than once costs you alot more in time and materials than doing it right ONCE. Hell, I have spent over $100 in synthetic lube for the tranny alone now...%)
Good luck.