Just as an update guys. I went to Ralph Moores over the weekend to get my car looked at. Found out my windscreen wasn'teven holding on to the car in the right hand corner. The seals were all gone on that side. Had it pulled out, cleaned up and placed back in with new clips and sealed back. Metal surrounds fit perfect now. Gotta touch up the paint now though because the metal wouldn't secure to the clips because it was bent out of shape.
Back glass had the clips and seal replaced and things sit flat back there as well. Need to touch up that paint as well though.
When I drove it home a lot of the sounds I thought I was hearing from the t-tops weren't there any more. Maybe the windscreen not being secure was causing flex around the t-tops. Or it was the windscreen making the noises. Either way it's one more thing fixed.
We did find out though that the Transam has a bit of rust around the front and rear glass. It's never ending. I know she needs a paint job but I was trying to prioritise the work.
Also got the suspension to look at too.