First post here, but have browsed a lot.

Have a 1996 XP, personally rebuilt engine back in 2011 season because of clogged oil injection filter. Rebuilt engine, carbs, cleaned everything, all fuel lines replaced and it ran great 2011 and 2012 season.

2013 season, couldn't keep battery charged, found bad rectifier, replaced and then found bad main ground from battery, added additional ground. Ever since this the ski has run bad mid range. It bogs out of the hole and runs rough/surges mid range. Still has good power up top. I have:

Rebuilt carbs (they were clean) and replaced diaphragms
Bypassed fuel selector valve
Replaced spark plugs
Compression is good (over 150 psi on both holes)
Checked for cracked fuel pickup
Checked RAVE valves
Played with high speed screw (took caps off)
Trimmed tips of plug wires

I am going to swap the grey electrical box that houses the rectifier, CDI unit and everything else with a friend of mines to see if it is something electrical.

Any other suggestions?
I am at a loss.