Altering alignments by each stage

[[An...]]

Is there a way to manually change the alignment of multiple changes? My prealignment gets me to close to where I need to be, but each part is off slightly. I can easily fix one stage via the "set Matrix" alignment, but this hurts all the other alignments. Is there a way to use the "Set Matrix" alignment on each stage individually? 

 

Thank you!!!

[[Ma...]]

How specific is that prealignment mismatch?

I had no luck to fix prealignment on almost symmetric or rotary model.
Would simple bestfit help?
Like:

• do prealignment
• bestfit of selected part of a mesh based on prealignment
• next alignments based on bestfit.