What are the mods that can be done to the intake and injection to make it more gooder?

Well, there's a few simple and cheap things to do as far as intake goes. First, take the air cleaner lid off, and look for tow things: One would be on the lid, the big bowl shape that might be attached to it needs to take a trip to the scrap pile. This has been nicknamed the soup bowl... It isn't on every 6.9 or 7.3 IDI, but is on some. The other thing, if you don't have the soup bowl, is the bottom of the air cleaner. The hole to the intake may be restricted in size to nearly half the size of the intake. My 86 had this restriction. I cut it out to the size of the intake. My dad's 84's have the soup bowl, but not the restriction.
The next thing on the intake is to do away with the plastic section that runs by the power steering pump. This is known as the pancake section. I put 4" pipe from the plastic hose to the back of the rad support. I hope to get around to finishing the project by opening up the rad mount for air flow, then hook it up there to get the cold air ram effect from the grille area. Some have used heater ducting to seal to the front and get air from the grille area.
Otherwise, the fuel screw and timing are the only other options topside to play with. Before you get to playing with the fuel setting and the timing, you need to ditch that crappy restrictive factory 2.5 exhaust and go 3" minimum. You can use a powerstroke rear system of the same body, but to get full effect, the y-pipe needs to be modified as well. I reworked my y-pipe so that the passenger side flows straight into the rear pipe, capped it where it went into the left pipe, and made the left pipe angle into the rear pipe at the same place the passenger pipe came into the rear pipe. I got used but good pipe from a heavy truck salvage yard, to them it was just junk, but I was able to find plenty of good 3.5 pipe to make my whole exhaust, even with a 4" tip. Much of it even has a Ford stamp on it...I started out with 3.25 at the front, fabbed my own high flow muffler, and used a 3.5 outlet on it. Works pretty good.

Exhaust won't be an issue, going with a pair of 4" stacks after some 3" off the manifolds, also have thought about a pair of headers, just need the site (I know its on that "other" place).

What can I do with timing and the fuel screw? I know its not much of an adjustment on the screw but I've never read anything on adjusting the timing, also any shots of said soup bowl?

Stan's Headers is the only place that makes them for our IDI's. I would wait until after you get the intake and exhaust on to tinker with the IP. You can turn the fuel screw up a bit, about 1/2 flat at a time to be sure you don't overdo it. After opening it up though, you could probably get away with one full flat.The timing is set by hooking up the cold start advance to power, then bump it up until you hear the "powerstroke rattle" and then back it off just a shade from that. Otherwise, find a good diesel shop that has a clue about older diesels, and have them do the luminosity probe timing set.

Whats a luminosity probe timing set?

you can also get marine injectors

The luminosity probe is a tool that is put in place of a glow plug and reads when the cylinder actually fires by reading the light from it, hence the name luminosity (luminous, light) It is the most accurate way to check the timing.

Damn, how did I miss that question so long? Still is hit and miss with the post notifications...