It sounds to me like you've missed something in your diagnostics. I am pretty sure that is has been established that you do not have a P7100 Injection pump. I've been down inside of the P7100s and I can assure you that you cannot rebuild that yourself. I am going to go off the assumption that the general concept of the inner workings of the VE pump is similar to the VP.
On the P7100, there is a neoprene like bushing at the very back of it that is blow molded into the aluminum housing. To replace it, you have to carefully melt the old bushing out completely, the using special tooling and dues, you have to blow mold the new bushing back into the housing. One imperfection in that bushing, the pump is junk and you start over. That bushing is what allows the pump to build pressure to do the pumping. Here's the past that shucks for you... That budding is lubricated by the fuel pumping through it, you run it out of fuel, the metal shaft scores the bushing, now the pump is shot. When you are making your calls, find out if your pump is lubricated the same as the P7100, and ask if it has the neoprene or plastic like bushing in it that the main shaft rides on. If it is similar in this respect, just offer the new injection pump. Don't disassemble yours, the core charge is outrageous!
Now, while your waiting on your new injection pump, let's put the K.I.S.S. method into play. The 6bt is the poster child when it comes to engineering with this method in mind. Fuel+Compression+Air, and it will run.
First, because you mentioned rust in the fuel. Pull the tank, take it to your local radiator shop and have it boiled out. Have them pressure check it and seal it while its there just to save on hassles down the road.
Second, since you will have your sending unit out, remove the in tank lift pump and fab you up a piece of brake line to bypass it, (install an in tank filer if you can, or a "sock" as they are sometimes called), run a frame mounted lift pump with a fine filter between the inline and the tank. Check the inside of your steel line there, if there is any rust build up, just replace the line, expect at that point that you are replacing all your fuel lines. You can wire the in line lift pump to your factory wiring harness. Test the sending unit with an ohm meter. As you slowly raise and lower the float, your readings should be steady and consistent, if they jump around, replace the sending unit. (Keep a spare lift pump behind the seat...you can hear these run. If you don't hear is running, quit cranking. You'll know why when you see the price tag on the IP.)
Third, after inspecting the steel line from the lift pump to the plastic line at the engine, and replacing it if necessary, you want to look real close at the plastic line. Look for dirt buildup, especially near where the plastic line comes close to the bell housing on the transmission. It is common for this line to get pinched if that tranny has ever been out. Replace if necessary. Be sure it is clear of debris as well. If you find any blockage, replace it.
Fourth, you are now to the filter housing on the driver side of the engine block. Check your threads on the in and out ports, carefully remove any burs for these threads. If the threads are stripped, replace the top housing. The lower housing, I would replace with a see through type. This will save you future headaches on fuel issues. If your pocket book can handle it at this point, I'd penny up for a dual filter housing here, if not, just make sure you have a quality filter in here. Check the remaining lines for crossed threads and blockage. Replace as needed.
Fifth. By this point, you should have your tank back. Get it back in the hole, and hook all your lines back up until you are to the second filter housing (the one on the engine). Put at least 5 gallons of fuel in the tank, you do not want to "bump" the ignition key to get the pump to run because you'll screw up the timing on you IP. Instead' run a temporary hot wire to the lift pump. Turn the lift pump on for 30 seconds, let it rest for 30 seconds. Cycle the lift pump this way until you have fuel at the filter housing on the engine. Now, put your filter in and fill the filter housing with regular automatic transmission fluid (I've always used Dextron III) and screw it onto the upper housing. If you hold your mouth right, you won't spill much tranny fluid.
Sixth, cycle your lift pump until you start getting fluid out of your lines that go to the IP. Stop here until you have your IP installed. If you don't get fuel here, check your shut off valve again. It should be near the big filter housing on the side of the block near your throttle linkage with one, maybe two, wires. It should have a soft rubber boot on it and will probably have a rod coming out of it's center. If the boot is cracked or torn, replace it. Find your wiring diagram, run your hot wire to it, if it has a second wire, I believe it goes to ground (again, check diagram). When you power it, the rod should move and you should here it click. If there is no rod, gently put your finger on the center of the boot, you should feel it move. (I believe the road allows your throttle linkage to function the the shut off is in the "open" position.)
Install and primer the IP per the instructions from your supplier. Your lines from the IP to the injectors should remain loose, but started, until all are started. Prime your injectors per your suppliers instructions.
If all this checks out, your truck should run. Once running and all injector lines are purged, double check the #1 line a few more times to ensure its not spitting air at you. While not advised, if you must use eather to start the engine, spray the eather onto a shop rag then hold the rag over the air intake. Do not spray eather directly into the intake.
If you can't get it running with the above method, take it to a diesel shop. And NEVER run a Cummins out of fuel. That injection pump can't handle it, especially with this ultra low sulfur crap we are forced to run now unless we can make our own.