My symptoms cetainly sound similar. I am wondering why the problem would go away when it gets warm? Matbe because the metal is expanding and sealing up the leak? Also can you discribe the vaccum pump setup a little more? What type and where you hooked it up?
The reason I used a vacuum pump for the air source is because I already had a vacuum pump, a fairly good size (1/3HP) one, with an adjustable output. Vacuum pumps can be used either to pull or to push, but they don't make a huge amount of pressure. The output of mine is threaded, so I just put a gauge on it with a bleeder screw and a hose barb, and attached a piece of fuel line to the output. I can bleed off a little pressure and adjust the output pressure with the amount of air I let out. I think it's fairly important to use low pressure on the fuel lines--the supply line isn't pressurized while the engine is running, and I thought I might create more leaks if I put high pressure air to it. I used only 10 psi, but I think even 5psi would be plenty. If you don't have a plug to put in the other end of the hose, you MUST open your fuel tank cap, or pressure will build in the tank, forcing fuel through the supply line and all over whatever is underneath it. Don't ask me how I know. I got under the truck with a headlamp on and traced every connection point where the lines transition from steel to flexible. I was replacing the rear tank at the same time, because it had a very slow leak in it, so I had an easy time making sure the air leak wasn't from the tank connection. You only have to pressurize the supply line. If you have a leak in the return line, it will just drip, but not allow air to enter the fuel system. A diesel drip is another problem all together, but a LOT easier to find and correct.
My leak seemed pretty small to me--just a small wet spot where a factory crimp-clamp wasn't holding tight enough. There was a very slow drip in TWO spots. At the tank switching valve, the supply line is the one closest to the frame rail. You have to be VERY careful with the pollak switching valve connections. The plastic gets brittle after 15+ years, and WILL break if you put any amount of torque on it. I broke mine. Expensive lesson. There is a great supplier of them, Kascar, on ebay, they are the same switching valve used on the military Humvee. Kascar is a supplier to the military. It was under $200, but I shouldn't have broken it. The Ford Dealer wanted something like $350. I don't remember exactly. Anyway, you have to make sure every connection is holding pressure. I replaced every connector to the pollak valve also. It is nearly impossible to remove the factory connectors without breaking them.
The factory line is braided steel covered in some sort of rubber with a teflon liner. Not only is the liner very difficult to keep from bunching up around the hose clamp and bunching up inside the tube, but I simply couldn't get enough clamping force with little worm-gear clamps to keep it from leaking, so I replaced the factory flexible hose with fuel injection hose. Regular old fuel line is not enough. For what it's worth, 5/16" will work for both supply and return lines, you just have to be patient with it and lubricate the barb of the factory steel line as well as the click-lock connectors for the pollak valve. I found that 3/8" i.d. fuel injection hose is too big to get a secure connection around the steel rigid fuel lines. I over-torqued a couple worm gear hose clamps trying to do this. Don't buy cheap hose clamps. You DO have to use 3/8" i.d. line on some of the connections around the fuel bowl. As far as the bowl is concerned, I ordered a complete o-ring kit from dieselorings and covered all possible leak sources at the same time. There's no way to be sure otherwise.
This is a big project, and will take more than a couple hours when you factor in the normal amount of time spent cleaning off the dirt and road grime from the hoses to actually SEE if you have a leak, the unforseen diesel spills, torqued out clamps, and the difficulty of working around the frame rail supports that completely surround the pollak valve. To say it is a pain in the A$$ is putting it mildly. Only one of the two leaks I found was enough to actually show up on the fuel line before I put pressure on it.
I don't know for sure that this is your problem, but the only way you can get air in the fuel line is from a leak. I had to go through all this to ensure there weren't any leaks. To be completely honest, I did this all twice, because the first time I didn't fix my problem completely. That's why I got so obsessive about every single connection. I found the second leak after fixing one, which seemed to make the problem go away, then all the sudden getting stranded on the highway. All it takes is a little tiny leak for air to build up. The diesel shop I went to about my problem told me it was the fuel pump. After replacing it and still having problems, I grabbed the bull by the horns. I don't regret it. Problem gone, and now I know the fuel system very well, and can diagnose other issues a whole lot easier now.