Wes,
Sorry for the lateness in this response, as I hardly come to this board anymore after getting rid of my 2003 5.4 and 1999 4.6 powered F150's and retuning to my 1993 F150 with the 4.9 and 5 speed, but I do have some very meaningful experience with the 4.9/300 6 from years of experience.
The best thing to do with the 300/4.9 for good performance is to improve the exhaust system. I personally use the EFI exhaust manifolds that come on the '87 and later 4.9s stock, then use a Walker/Dynomax #15022 catalytic converter (dual 2" in/single 2.5" out) and 2.5" pipe to a 2.5" in/out muffler (currently a Dynomax #17788 Turbo muffler), and a "Y" connector to dual 2.25" pipes exiting out the rear. The exhaust sounds like an old P51 Mustang aircraft; that is the best description I have for it. And, it will give you much better performance and fuel mileage (about 2 MPG in my case).
On the intake side, go with the K & N FIPK kit for better airflow. The stock system is quite restrictive. This will give you far better performance. I know that prior to changing my intake system, I had to downshift into 4th, and sometimes 3rd, just to get up some hills north of Phoenix; today I can climb up those same hills in overdrive with no problem. I also get another 1 to 2 MPG improvement with the FIPK.
The ignition system is fine in those years. The only thing I would recommend is to use Motorcraft or Autolite Copper Core plugs; anything else is a waste of money on a 4.9. I do recommend a good cap, rotor and wires, usually Accel or MSD cap and rotor with Taylor wires, and an Accel or MSD coil. Also, bumping the initial timing up by 1-2 degrees in increments and testing for ping is good for both performance and mileage. Stock initial setting is 10 degrees, I am currently using 13 degrees initial, and picked up about 2 MPG over stock, along with more pep during acceleration. 16 degrees started to ping a little on grades under acceleration, so I backed her off to 13 degrees.
Double check the measurements of the radiator core, and see if the Flex-A-Lite #295 electric fan will fit your radiator core dimensions (it should if you have A/C). This one change brought another 1 to 2 MPG to my F150.
All of this in consideration, I now get 18 to 20 MPG in the city, and depending on terrain of the highway can get anywhere from 20 MPG in hilly terrain to 24 MPG highway at a steady 65 MPH on the flats to Tucson or Yuma.
1993 F150, regular cab, short bed, 4.9, 5 speed, 3.08 gears, 255/70 15 tires. Only other things done are to add DJM 2" rear drop shackles, stock aluminum wheels, and a tonneau cover that added 1-2 MPG highway.
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