I'd recommend something facing the rear of the vehicle, like the first picture Angus posted. If you have it face towards the front it will most likely get air pushing down into it as you're driving, and defeats the entire idea of cooling the engine.
Another idea for the intercooler is to custom making fittings to mount it where the stock muffler would be (this would obviously require you to also have an aftermarket, custom exhaust. This is similar to how the MK3 turbo kit has it's intercooler mounted. I've also seen it put into the trunk area, which I'm not so sure about since it wouldn't have any air flow without further modification.
As for the your vacuum lines.
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Originally Posted by kevin mr2 1985
now this bracket is off of the firewall between the driver and the engine bay. i need to know where these hoses go? i do not have cruise control or ac any more. if that helps.
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That kinda looks like the saucer from the EGR system on my N/A. If that's the case most of those lines would go into the throttle body somewhere.