if you have an 1/8" gap, I would think it will leak. But like you said, I guess, try it out.
Maybe you need to open up or slot the 4 holes on the intake manifold where the exhaust manifold bolts up to? This will allow the exhaust manifold to center up flush w/the intake manifold flange. Might need to trim/grind on your intake & or exhaust manifold where it was hitting before.
Yes, you can take out 1 high beam headlight for cooling & maybe ramair to the turbo?
As far as turbo location, make sure you have enough room all the way around the turbo, the stock 6 cyl mounts move excessively, also, if you install a physically larger turbo, you will have room for an upgrade if you are wanting to do so later-on down the road.
Also, make sure the oil drain line from the turbo is high enough & will put the drain line @ a good angle to drain back into your oil pan.