I was getting a lot of problems with my bake, the edges of my topology was showing and I was getting artifacts of darker splotches around the ends of the clothing.
This is because I was making mistakes in my settings. Instead of having it match to the names of my assets such as matching _low with _high it was using any. The other problem was I was using the wrong resolution, which I fixed by turning it to 2040. I also tried turning anti aliasing up to 16 however this didn’t make a noticeable difference. I found the thing causing the main problem of the edges of the topology was because I didn’t shade smooth in Maya before exporting my low poly version.
The mesh after making corrections:
To get rid of the splotch artifact on the shirt, I opened the low and high poly meshes together in substance painter, and used the move brush ad the inflate brush to match them more closely together.
The only other artifact I have on the bake in on the trousers around the tail, however I think it is ok to move on as the dark texture will conceal it.
Looking back, I think it would have been better to duplicate my high poly asset in Zbrush before remeshing it, so I can compare it with the low poly version and make sure it matches at an earlier stage, rather than having to go back and forth. I also should have established the flow of topology I wanted in Zbrush before Zremeshing the clothing. This may have prevented some distortion and would have made the assets much easier to UV map.