Weired Vacuum/Exhaust problem after H/C/I install

First off, thanks in advance for any help I get and YES I did use the search forum but had no luck.
Just completed a total engine rebuild on my 89GT and having a weird vacuum problem. Here is what all I did to the motor; rebuilt the short block (kept everything stock), put on GT40 heads, TFS Stage 1 cam, 24# injectors and put on a ported GT40 intake. I have a 70mm TB with a 73mm C&L mass air calibrated for 24's. I also removed the air pump, p/s and a/c. Am running a electric fan, under-drive pulleys, swapped to a 130 amp alt (which isn't charging) and did a five lug/rear disk upgrade.
Here is my problem; I only have 10in of vacuum @ idle. I have adjusted the valves 3 times, checked for vacuum leaks (don't have any that I can find), checked my timing, made sure my firing order was correct, reset the computer and all that other fun stuff. The car idles fine and seems to be responsive when I snap the throttle. Now here is the weird part, when the engine is cold and I pull a vacuum lime off it runs like crap and loses vacuum. If I do the same thing when the engine is warm the vacuum goes from 10 to 15in and the idle raises to about 1500 rpm. I have never seen anything like this before and am totally frustrated by it. :bang: I have to drive it to CA in a week and a half and as it stands now I cant because I think this is part of my brake problem. One more thing, for some reason I decided to check and see what the exhaust felt like coming out the back and no matter how long I let it run the driver side bank blows cold and never gets hot like the passenger side does.
I hope I haven't confused anyone, if so let me know and I will try and explain better. Thanks....-J-
 
Well I just fixed the charging problem and no change. Even that was a weired fix, on the back of the instrument cluster where the grey plugs goes, one of the copper tapes was bent back. The only reason I thought to look there was because I noticed the the amp light wasn't on when it should have been. I'm telling you this car has thrown me for more loops than anything I have ever worked on before.
 
just a wild chance, but I chased a vacuum issue for over a year, and finally traced it to a dead (fake) port on the front of my explorer intake. As well, some of the other ports were carbon'd shut about 90%. try taking vacuum hoses off and sucking on them, if it's not real easy to suck on them, your hard lines coming out of the upper may be clogged...if it's a new intake then you're probably fine.