Install Problems Yesterday

So yesterday I started my install of upper and lower intake manifold and am now faced with a couple of questions. The first and most important question is one of the bolts used to mount the lower to the heads broke off inside the head. After spending several hours trying to remove it, it has become blaringly clear that the head is going to have to come off for either replacement or to take it to a machine shop. Does anyone have any experiences similiar to this? What worked best for you and where can I get the exact head replacement so I can replace just the one side?
Now, as I was removing the upper, I noticed a number of differences between my HO upper and the cobra upper I bought. First thing I saw was on my HO upper there are two vacuume lines that connect near the throttle body and on the cobra there is only one. So what happens to the remaining vacuume hose? Also I am guessing I will need new bolts to connect the throttle body to the manifold because the existing ones are very rusted and dont look like they would work anyway. Another thing I noticed was that under the upper there is a vacuume hose that connects on the front of my HO upper but on the cobra it connects on the back side. I guess what I am getting at is, are there any documents for swapping from my upper to the cobra since they have different vacuume setups.