Firstly, put your truck info in your signature, that helps ALOT when diagnosing, or guessing about problems.
Sounds like you have a lot of little problems.
The start up problem is classic symptoms of Air Intrusion. That will also cause the surging, and likely some fuel starvation. The first thing to do, is replace your return caps/lines/orings. PM type4, he sells a higher quality kit than any parts store, and for less to boot. Next, if you have a 6.9, read up on the Stanadyne water separator in the tech section. That's a common failure part. If you have a 7.3. There is a check valve on the fuel filter head that goes bad, and will let fuel drain back to the tank. Causing that symptom.
Next, it sounds like you're fuel starved. Change the fuel filter.
Next, have you ever had it timed? Timing makes a HUGE difference in how these trucks run. Never trust a shop that says they can time it by ear. Ear timing is, at best, just a way to get you moving until you can get it really timed.
Now, a dead lift pump will not pump enough pressure. You should see about 7psi after the filter. Also, check your oil and sniff it. If it smells of diesel, or if it's getting higher, then your lift pump diaphragm may have ruptured, and is now filling the crankcase with diesel. (that's a REALLY fast way to loose your main bearings)
Take a look at all of that before you start worrying about the IP and injectors.