Sorry I just have to throw a few pennies into this conversation as they are needed.
First Plugs and wires.....Aldive summed it all up ....I will add that the Motorcraft Plats that came in our engines are my recommended plug....new ones of course. Wires? Doesn't really matter that much just so their decent quality. Afterall this isn't a race car with a hypo ignition system.
-Intake/air filter...
You have a few options for an open air intake. I really won't say one is better than the other just pick what you like. The main purpose is to smooth out the flow of air in the intake tube and make the filter able to pull more air. KKM is a cheap adapter for adding the conical filter. The K&N or MAC type units replace the whole tube as well as adding the open air filter.....
...Realistic gains....Throttle response is improved and maybe a couple ponies...Sure sounds mean though
-Throttle Body..
BBK is currently the only manufacturer that I am aware of making a tb for the OHV. It was designed for use in their out of production instacharger kit. It is a 66 mm unit which in reality is a bit big for stock internals and heads, but works and is available... Take a dremel to that plastic upper intake and port match it to the TB as well
...Realistic gains. Maybe a poney or too and a bit more throttle response. It also seemed to move my powerband up a bit higher, though I could be tripping.
--Mass Air.....
Don't bother. The Pro-M is not woth it in my opinion. Granatelli makes another for the OHV, but realistically you are better off keeping the stock unit. The Stock MAF is a 70 mm unit which is more than adequate for our engines even with a good bit of tuning. In addition the electronics are easier to deal with from a tuning perspective. C&L is a potential option but none of the OHV crowd have gave it a whirl to my knowledge.
---Pulleys
To my knowledge there is not a set made for the OHV 4.0
-As to the upper and lower intake your kinda stuck unless you would like to look into swapping for the early model OHV aluminum intake and porting it considerably.
-Heads are still floating around out there. There is no per say aftermarket heads, but there is a guy over on ranger powersports that used to build a stage 3 head......Occasionally they will show up used..or you can have yours spend a bit of time at a machine shop..
--Anything exhaust/header wise will be custom....Though JBA used to make headers I am not sure if they are still in production
--Lastly is the tuning. BamaChips is the way to go....
Now you can get inside that motor for more, but you had better have deep pockets. The above is a good start for supporting a bottom end build though and will cost you a fair chunk so you can budget for the bigger stuff.
If ya really want to have some fun start hunting for the long lost BBK Instacharger for the 4.0 OHV. They are around but rare.