Eric,

I just had an idea that might be worth checking first. You replaced the flyback with one that was a "mirror image" of the original, so you had to resolder some wires. Look on the schematic at the bottom winding of the flyback, the one with the width control (L15) connected across it. One end is grounded, and the other end goes back to the phase detector circuit. If the leads from this winding somehow became reversed, the horizontal output stage & width control would still work normally. However, the pulse going to the phase detector would be reversed in polarity, and would drive that circuit crazy! Since this was not an actual "exact replacement" transformer, the leads from that winding may have already been reversed at the terminals when you got it! Just a thought.