Maaaaaate. Good to see another person with an 88 NA Fairlane. Well from what i have read in my time on here and in my manuals, the NA Fairlane only weighs 1555kgs, so it so much of a heffer as what people have thought!
Onto the mods, well the first port of call is to ditch the transmission. The 3 speed is not built for performance, for $1500 you can get a tricked up hi-stall C4 3 speed transmission that should give you some good bang for buck. I would not upgrade the diff so high, like no more than 3.08 imo because the NA revs fairly high at 100 as it is.
Definately go the exhaust. In the next few weeks I am going to buy a set of Pacemaker extractors and get them fitted. Currently I have a 2.5in Mandrel bent, single muffler sports exhaust, it is nice and loud, turns heads. I also have the added benefit of an EBII 4.0 that I put under the bonnet when the old 3.9 crapped itself. Definately head work will help to make the 3.9 get up and move, Crow Cams seems to be the pick, their current cam, valve springs and cam gear kit for $1700 seems to be the go, with a reported 30-50rwkw increase, which is very decent.
If you put in an K&N Panel filter, then it would be advisable to go to your local Ford Spare Parts dealer and get an XH Ute intake snorkel. This is a wider intake by about double compared to the original NA's intake, this allows more airflow into the engine, and with extractors is a good combination.
With the few mods that I have done, I can generally keep up with most of the 6cyl boys in the club, even though I am hauling the extra weight.
Hope that helps,