You may be missing one of the check valves in the system. I have them all in mine because I pulled a complete umm..harness ( looking for term here) of the vacuum tubes from a 305 car and installed it on mine. However, I am having the same issue you are right now. I am wondering if I have a bad vacuum motor in mine, but won't get to it until after the paint is finished and the car is ready for the interior. As for where to get them, that I do not know, but I can tell you how to fix them. If you have a cracked one, find some washer fluid lines and you can cut a piece of that to use as a sleeve to splice them back together. Use some silicone on the two tube ends to get a perfect seal.
Oh, one more thing: I was junkyarding today and looked at the vacuum tubes/hoses on a 79 Malibu wagon to see how they were hooked up. The vacuum source they all plug into is the port on the manifold between the back of the carb and the distributor. This is a fairly large port, so it is possible that it is needed to provide enough volume for the systems that are connected to it. I dunno. Mine gets vacuum to the motors under the dash and they still won't all work. I am wondering if in my case the fact that they were disconnected for the last 10 years has something to do with it.
Yet another thought is that the vacuum line leading in to the ball was black on the Malibu I looked at today. Maybe if I get ambitious tomorrow I'll take a pic of my vacuum line placement for you. Oh, and the Chiltons and Haynes manuals will not have any of this information. You really need to find a complete set of the factory service manuals from GM to get the diagnostic stuff on these systems. The small books at the parts store mostly cover maintenance and the basics. The three book set I have is probably 3-5,000 pages long and covers EVERYTHING. Not all of it is G body--it covers B and E bodies too-- but it covers every single option and system for each model covered.
Still not finished... My heater control valve is not located on the intake manifold, but this is the stock location on most SBC G bodies. I used the Buick V6 valve and location which is right before the heater core. I did this because it allows more clearance for the dual snorkel air cleaner and because my vacuum lines are only long enough to reach that location. If you have the short hose set, you can just get one for a 85 Cutlass Supreme with the 3.8 V6 ( VIN A) and it will work just fine.
As for the trans lines, try wrapping them or making a heat shield to reflect radiated heat away from the lines. Use stainless steel if possible when making it as it is more heat resistant than regular steel and does not need to be painted.