Well, assuming you got an actual HRpartsNstuff trans mt, it should put the height right where it was from the factory. It will appear higher than before, since you & 100,000 others have old soft rubber mts & this corrects it.
BUT, if you have the imitation copy of our trans mt (looks pretty much identical), then it is NOT in the right spot. They use 1/2" thick stainless (saying it's better) when it should be milled down to 7/16" to be at the right height. That takes extra effort & costs more, that's why they don't do it. We make stuff right, that's why we do it.
Being that you seem to have unplated bolts going into your trans, that makes me wonder if you don't have one of our mounts (since we include new plated grade 10.9 bolts). You need to use the longer bolts since the mounting plate is so much thicker than stock.
As for the new exh hanger, it should be the same as stock or so close it shouldn't make a difference. And you are right to leave the spacer out when using the hanger.
As for a fix or improvement to your situation, if you have the imitation copy version with the 1/2" plate, I would get it out of there. That also throws off your pinion angle & puts more stress on the u-joints. I would like to know if that is the case, especially if it was sold to you as an HR item. The best way to tell is to measure the main plate & see if it is 7/16 or 1/2 inch thick.
You could also loosen the bolts on the loop & slide it to one side a little & re-tighten. That will make it look & fit a little better. You could jack it up a little & bend the mounts/loop slightly, but don't go too far or the floorpan will bend & the seats will tip out & look weird. Basically, if the d-shaft doesn't hit, it is fine. Could be looking at some worn body bushings too, but that wouldn't explain the change from installing the trans mt.
Hope that helps!