I just looked at the Schumacher directions on line and your pictures. First you do have the mounts on correctly, they should be behind the block ears and you can't really swap them side to side because of they appear to only have 3 holes and one one would end up not being used on each side and you would have used only 1 bolt instead of 2 on the forward mount .

First you should have not modified the trans mount as said , the trans locates the engine front to back , change the trans mount to one that is not ovaled and go from there .

Looking at your drivers side picture the rubber mount is not 90* to the bracket, everything I saw says it should be and it doesn't look like there is a big enough notch in the K frame mount for the oil pump.

I'm not sure about the pan but the Pro parts headers were NOT designed to be used with the Schumacher mounts so any dimpling that needs to be done does not surprise me. I'm pretty sure you would run into a ding here and there with them on a motor plate , I have yet to see any set of headers that didn't need a whack no matter who made them and what they were installed in.

If anything I would be slotting the holes on the K frame to make it fit based off correct trans mounting. As close as things to begin with, if the trans mount was not modified then the headers would probably clear, pan to, change that and work from there.