Plan B on the shock absorber front arrived today. Its from a new 2013 ZX6R and was removed prior to putting the bike on the track, so zero miles.
The shock is longer and the reservoir is situated much higher up than on the R6 shock so this should hopefully solve the chain clearance issues.
The spring rate is slightly lower than the R6 shock, hopefully this shouldn't cause an issue. I need to strip the spring of first before I can put the numbers into my spreadsheet.