No exhaust system can cause a bunch of odd things. (Besides hearing loss...) It might be the source of your trouble. These little 4 banger Isuzu motors do run better with something behind them for exhaust, especially in the low end of the RPM range. I've never run one for very long dumping right out the manifold or header, so I'm not sure exactly what kind of difference we're talking about here.
I don't recall ever seeing anyone post here that they did an actual check of the ratio (turn the yoke and count wheel revs). Somewhere I have a rear axle that came out of my 77 with different gearing though. The truck came with an auto trans(which I yanked out) and the pinion bearing went on the original rear. When I replaced it with one from a stock stick shift truck, I could tell the difference in the gearing. SO... yeah there are really different gears for different models, but I'm not absolutely sure what is in the 4x4s.
31" tires should put your speedo somewhere around 12-15% off, maybe a bit more. So at a reading of 50, you're probably doing something like 57-58. My 4x4 with ~28-29" tires is just about dead on 10% off. 50=55MPH. Find a speedo check zone on a nearby interstate, or one of those mobile speed displays the cops put out to show you're going too fast. Topping out at 50 seems like you might have a problem somewhere. My tires aren't that much smaller and I can get 70-75 on the speedo(80+ in reality), and that is with a motor that hasn't had anything major done for it in the last 10 years.
Finally the air cleaner bit. The stocker is held on with a pipe clamp sort of deal around the carb neck and bolts to the valve cover. In order to use something that is setup for a through center bolt, you'll have to get creative and fab something up. Personally, I'd just buy a K&N filter for the stock cleaner. If you're trying to dress it up, sand the stocker real well and shoot it with some paint to match your tastes. Just stay away from the hobo chrome.
