In your first image it appears you have planar faces which should easily be replaced with Delete Face with Heal option.
I would then send back to Repair or Construction environment or to STEP and back in for final clean-up
In second image you have surface bodies. I would get these to solids and then do above steps.
Attach your files here. I am a little surprised that Stitch didn't remove the boundaries between faces (were appropriate).
hello
I am sending a sample of the original file.
I remember the original file has thousands of components similar to this (about three thousand members)
good luck