I thought I'd post a followup for future reference for anyone looking for a solution to the problem I had.
The header bracket does have slots that allow for vertical adjustment. This is the only adjustment for the header pipe relative to the engine and seems to be the major control for clearance at the tranny cross member. To adjust this (once the two 13mm bolts are loosened) you will need to pry in a way that exerts pressure between the header pipe and the engine-tranny assembly. I didn't realize this originally and just went between the frame and the pipe but I only moved the engine. This requires a lot of force because you are going against the 90 degree bend in the header pipe and there isn't a lot of give there. My next try was to pry at the tranny drain pan but again I couldn't move it enough. I think I was just picking up general give in the header pipe. My final and successful attempt required a large (2-3') sturdy crowbar, a piece of 2x4 long enough to span from the bell housing to the tranny pan and a support for the other end of the crowbar to hold it while I tightened the bolts. I used the 2x4 as a fulcrum because there weren't any good pry points on the bell housing because of tranny oil lines, etc. I worked from under the driver's side of the car and could actually see the bolts and the slots on the bracket so I could see how much it moved. Once I had it pried to where I wanted it, I put something between the floor and the end of the crowbar to hold it in place and tightened up the bolts. No more noise!
I'd be hesitant to eliminate this bracket based on my experience but there may be something strange about my car (maybe a bent mounting point or something) that requires it. I had no problems until I changed the engine and tranny mounts- my guess is that I shifted everything up enough to occasionally make contact at the cross member
Hope this helps someone.
Lyle
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