Just caught up with your progress and challenges Darren. A real 'Labour of Love' and very well executed work!.
It's a shame you couldn't obtain the original tyre size and a rough estimate is an extra 9" of machine travel for each rpm, or 24% increase in speed, so your attachments/speeds will be less effective and you may have to break into a 'Canter' behind it .
As for the Shaft wear, with the need to fix it one way or the other, I would look to replace the shafts.
Not knowing the lengths of each one, or what the metal 'Hardness' figure is, it would not be as difficult or more labour intensive to grind off the Sprocket welds, mark up and re-weld onto new shaft(s) after milling the Keyways and pin locations.
Treating to the original RC Hardness may not be required if precision ground Silver Steel is used, as it is around 27 RC hardness in it's supplied, machining condition.
A 13" length of 1" dia (+/- 0.0005") is £12.27+ vat....... longer lengths avail. Correct Bushes can then be purchased........ I'm not an expert though!.
I'm sure Jim Beacon will provide you with good/better advice and looking forward to seeing your progress.
Glad to see the the Mk12 from John/Alan has found a very useful home.