Joel,
My LS7, transaxle adapter plate and brackets were installed by Superlite. During a visit pnut asked me where myshift cable bracket was... I didn't know that I needed one. I bought one, but I couldn't get it to fit because it was hitting the rear suspension cross brace. After speaking with several SL-C builders with Ricardos, they all had zero issues with theirs and significantly more space between the transaxle and the cross brace. Allan looked at it and told me my engine wasn't sitting level. We put a digital level on it and it was sloped almost 3 degrees upwards towards the back. We compared my brackets to the brackets on the Graziano car that's he working on and they appeared exactly the same. I called Superlite and explained all of the above, but they insist that I have the correct brackets. It would be nice if there were part numbers or some other way of knowing exactly what's installed.
I brought the car to a race-car fabricator last week. The bracket / adapter plate bolts were hard to remove and the fabricator asked if the adapter plate was threaded. I told him I didn't think so. In any event, the only way to remove the bolts was to use an large impact gun. All of the plating was stripped off of the grade 8 bolts, aluminum speckles were falling on the floor, the hole was "threaded" at an angle and the nice chamfered edge of the hole were jagged from having the bolts forced in at an angle. The hole in the adapter plate is so trashed that even when the bracket is removed the bolt won't slide through. In fact, I needed to use a socket wrench because it was too tight to spin by hand... I guess there's a reason a tap has channels to evacuate chips when threading a hole.
Here's what the hole looks like after removing the factory-installed bolt.
View attachment 97757
I spoke with Allan who's built something like 25 Superlite cars. According to him, most of the bolts go right through without issue. In a few cases he's had to loosen the three bolts on the brackets before tightening everything (similar to one of your pictures) and in a couple of cases he's had file the hole in the bracket maybe up to 1/8". So, he's never seen anything like what you're describing.
The only conclusion for my situation is that I have the wrong bracket. Even with the bolt being inappropriately forced into the hole, the location of the hole is off by at least half an inch to get the engine level and to get the shift cable bracket to fit. Since there are no part numbers to prove to Superlite that they installed the wrong brackets and they likely don't have any Ricardo brackets sitting around, I've decided to make custom ones.
If the transaxle plate is supposed to be a stressed member, then the manual should point that out. I just checked and it doesn't.
The first thing that I would is validate that you have the right bracket (I assume that they must have 6 or 8 versions of that bracket for different cars/transaxles). The easiest way to do that might be to trace, scan and email it to someone who has what you think you're supposed to have. If you have the correct bracket, I can't imagine that any amount of loosening stuff is going to solve that big of a discrepancy. At that point you would need to weld and re-drill your brackets or make new ones.