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I had a similar issue years ago and it turned out to be the brake booster. I'm not sure how to diagnose it but mine actually showed a brake warning light on the dash as if the parking brake was on. Just my opinion. Hopefully others will chime in.
pull the black hose off the brake booster and see if there is vacuum when motor running....... hard brake normally means bad booster, or lack of vacuum to booster. Since you just removed that line, I would check it for connection and pluggage.
well, you got that narrowed down....... take the hose off the motor end and see what is going on.... YES, if vacuum is completely lost, the motor should run rough... You also need vacuum to get the heater controls to blow air to the floor and dash.. no vacuum will blow only on defrost.. ........ I would pull several hoses off one at a time and check... check PCV hose to valve cover for vacuum from motor also.
I couldn't get ahold of any rubber vacuum hose Sunday so I used 3/8" id air hose instead, would you think that would be a problem? I'm trying to avoid pulling intake manifold for a third time