Hey @CanadianSpaTech,
Here is what I have found. I took the circuit board out and there are no burnt or dark areas. Everything on the board looks fine.
I put a new 20AMP fuse in and checked the pin out for the pump. High speed and low speed are both showing the required 240 volts.
I am beginning to think there is a programing issue. When the system starts it is showing 363 - r 5 - L 3. It is a YE-5 with 1 Pump 220V (3.01.0 HP), 4.5A Blower 110V, and Balboa CRT Ozonator Kit. On page 36 of the manual (http://www.geckoalliance.com/Documents/yseries_techbook_a_en.pdf) it is showing that the fuse (F2) which is the 20AMP fuse that keeps blowing is the low speed fuse, but the system still runs on low speed when that fuse is blown. High speed is the only thing that is not working. I am thinking the system is trying to run the high speed on fuse (F2) and low speed on fuse (F1) which is causing the overload.
Any help would be appreciated! I have worked on other systems before but never one with this complicated of a programing system.