The pump seems normal now although I was getting very nervous I'd done something wrong as it took a long time for the system to bleed and operate.  I now think the main issue with extreme nosie was due to the different length of releif valve springs. After reading, considering everyone's input and comparing the old springs to new I now understand the two odd springs were so worn they simply fell apart. This can't be good for valve operation and may be what caused the top of the first plunger to become damaged. The number one plunger spring perch was also missing the bottom collar. The pump seems to operte much more smoothly now but haven't put it under load to know for sure. I only do light three point work with it so it isn't like I'm working the pump hard day in and day out in the feild.