the gears and install (by his brother, me, adn him) were about 300 dollars. we replaced the whole rear axle (still like stock though) at the same time as well. all the parts came from a local junkyard. his engine has a modified intake, and a new cam. i don't know the total for those at all, but they probably really weren't worth it. his truck still is about twice as slow as my x, heh heh. i don't know what kind of shape you truck is in, but you could easily spend more on the engine (if you go inernal) then the whole thing is worth.
there should be some posts here about modifying stock airboxes. its not something i have done personally, both of my vehicles have gotten the fipk treatment, but as far as i know a series of half inch diameter holes all around the stock airbox will lead to better airflow and more performance. i know some people have also cut away huge pieces of the airbox, but in my minds eye i think the holes would be a better idea. do a search and see what you come up with, or just go experiment. good luck.
about the gears, that staight six is known for pulling power but 3.08s 35s and 4th gear is pretty impressive. it could be one of those ford mix-ups that are never expained. have you checked which gears came with yoiur vin number? it would be crazy if they were different than what the diffs say.
sorry if this pic worked, i just wanted to see if it worked, i've never noticed the attach file box before and wanted to see if it meant i could add pics.