I had the same problem and found out that I had the wrong windshield wipers.  I had put on a new modern pair and learned that the originals are much smaller.  The newer ones would not let the door close all the way.  Once I put a correct pair on, the problem was solved.  Maybe your issue is a simple as that?  BlueX22010-04-26 22:20:35

Thanks. I'll check it out.

If you don't have something in the way, there are two adjustments.  First, there are stops in the outer corners of the transmission that hit on the cowl.  There is quite a bit of adjustment there.  Also, the entire assembly is adjustable where it bolts to the firewall, including the ability to shim it forward or backward as needed.

Larry