"Would this vacuum problem prevent the fuel pump from even running? which is the original problem and why I need to jump it directly to the battery."
No. If the fuel stops flowing to the carbs, the fuel goes to a bypass route inside the tank.
I understand your frustration with winter coming on strong. Having everything disassembled makes it worse.
The fuel path for the 1100 is relatively simple with few components. The pump sends the fuel to the filter. From the filter to the vacuum operated fuel valve. From the vac.operated fuel valve to the carbs. When you get back to it, I would suggest trying the following.
Your pump is working.
Is the filter flowing fuel? Pull hose to verify.
Is the vacuum operated valve flowing fuel? Pull hose to verify.
If not flowing fuel, connect the output hose to the out put side of the filter, bypassing the valve. Run the pump for 20-30 seconds to fill carbs. Try to start motor.
I don't see how it could flow fuel if the vac. line isn't connected. I don't know of anyone around here modifying the valve to flow fuel without the vac. line. But, there is a similar valve on the 1500 Valkyrie. Those folks have figure out how to modify the valve for free flow fuel (by gravity) to an auxiliary tank mounted below the main tank. So possibly. But you said your carbs were dry, so probably not.
Here is an explanation with pictures. Takes less than 15 minutes when the plastic is removed.
Vacuum Fuel Valve Bypass Method ( ST1100 ) *
www.st-riders.net