Do the repairs one at a time.
The top cover & leaks are separate from the knocking pump issue.
" I am planning on changing the piston to a NAA with a O"ring is this a good move or not." Yes. And a new cylinder is also wise.
" Was also curious if I needed to purchase one of Zane"s jigs so that I can put everything back to together. " Yes. Buy it.
" Reason for rebuild is the pump is starting to knock after a good work out " One of my worker 8N's has been doing that for 10 years. I'd leave it be.
" she leaks down even with nothing attached." Rebuilding the lift cylinder will fix that.