The truck needs more plenum volume. But you can't get that.
I have a few 460 trucks in my stable, with lots built and sold over the years.

First, buy a set of L&L headers and get your exhaust guy to build a new set of pipes with dual cats into your 3" exhaust.
Then you need to get your oils swapped to synthetic. Engine, diffs, xfer and ps (ps is just for ease of driving) The engine will love it. I'm sure the xfer has never been touched and should be maintained. And the big one is diffs. (no royal purple because of oxidation levels rise fast in street vehicles) Find a good synthetic like valvoline or Schaeffer oils.
Next is high voltage ignition. Either MSD or Jacobs or whatever you prefer. I'm an MSD guy myself. Then gap the plugs correctly. I don't think the e3 you can but check and see.
Then look into gears. I liked my 410s but I also ran 255/85/16 so my effective gearing was better for hyway then you. (I'd go bigger tire vs gears. It's easier and if you need tires then you can change it easy) My 86 460 van with c6 and 355s got 11-13mpg. I know your efi and overdrive should be capable of that.

If you wanna crack the engine open then we will get into that later. Send me a pm and we will chat.

 

My swap to MAF on my 94 460 was probably more for the fun of it than anything else. I just happened to get everything cheap. The final results are not impressive. Main plus was that it started and stayed running at below zero temps. Also, low end was improved for slow wheeling. Other than that, the expense as it is now is probably not worth the effort unless you are planning to do some heavy modifying.