I was able to get help from the Vertex service department. The instructions they send along do not have appropriately labeled parts, no exact description of where the parts go and the pictures of the important steps are missing or hard to see in the pictures.
Sean was able to walk me through it over the phone. I gave some suggestions on how they could improve the instructions including having better step by step, better labels and better pictures and he said that was one of his projects he was working on.
I will say if anyone needs help I'm happy to help them to save them the troubles I had. I was afraid the unit was shot and I had to pony up for a new compressor!
Fortunately I was able to get the tiny parts all where they go. The upgrade rebuild kit is better in that the new piston housing is truly Teflon coated and the wear surface that protects the piston edge from the housing it rides in is now a true Teflon cupped disk. The old setup was not properly setup to prevent sticking of the piston against the housing and it sort of self destructed on the wear surfaces.
I would highly recommend anyone with a vertex system who has the old non-Teflon wear surfaces consider getting the upgrade kit and attempting it. Sean said on most of their accounts they just schedule it and do it every 2 years under normal use. I only run my diffuser at night and only in the hot summer months (maybe 2-3 months of night time run time) I noticed less boil, less PSI and a louder clatter from the unit so decided to do it at the 5 year mark.
I'm told this should last as long as the first, but to keep an eye on noise, boil and PSI. Variables that affect life of the components is heat (ventilation is key) and moisture. Check air filter too of course.
I'm going to lengthen my power cord and air hose and move the compressor box more into the shaded woods on the edge of the pond. I'm mounting it on a platform (cut off 55 gallon drum about 24" high filled with foam) and then put the cabinet on top of a Styrofoam sheet to prevent vibrations/walking away) that should float during any future pond overflow events. If time, I may add a enclosure that would put it in a more protected hutch or box, but with good air flow around it and it being in the shade all the time I'm not sure what else a hutch or enclosure adds except shedding rain.
If anyone needs help let me know.