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Hi Aidan,
Well, you are making some progress!
I trust that you did use a reticle eyepiece to test the bounce back and it perfectly centred in both axis. If so, great. Did you try the small slews test of a few arc-sec in all directions? If you see any backlash this could really mess up guiding especially in declination. (probably less so in RA as the gear is always engaged turning in the same direction. But, any RA backlash would possibly give you a problem right after an east slew.
Don't know what the bouncing up/down might be other than to remark that large scopes are much more prone to atmospheric motion. After looking through refractors of 5-6" most of my life I was quite horrified but what "in focus" looked like trough a 12" SCT. Are you thinking the bouncing might be vibration in RA? If so just turn off tracking for a few seconds and see if there is any change. Good luck!!
Peter
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