351w/fmx vacuum lines

I have a 1973 gran torino with 351w and i believe a fmx transmission. Both the engine and transmission have been rebuilt by local specialist shops. I only took pictures on my phone and didn't label thinks like I should have so I need help with knowing where things go and performance. My main concern is 2 metal lines on the driver side of the transmission. I know one goes to the vacuum module on the transmission but I'm unsure where on top and the other line doesn't have a fitting for it. The transmission shop said that the second line was for emissions and they blocked it off. The second problem is I'm having trouble with it bogging and dies when you shift it into gear. I feel confident in my timing and tuning abilities as it runs good and I can rev it up in idle. I feel like the second line has something to do with it not being able to move or idle in gear. Thanks for any advice in advance and sorry for it being so long.