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Cheers Sam (: hope you’re well
I just checked the numbers and I have been riding this bike a little under a cm lower than I should have so I guess that explains the feeling in the quads. Realistically the flared up tendon pain in the inner knee is probably because of the step up from 2hrs on a bike for almost two months to 200 miles in two days heh. Hopefully will just clear up as you say!
Copy your fit numbers as close as you can from the Kepler, if that is what you were bikefitted on.
Saddle positon should be set to be exactly the same. Height is easy to move over. The for/aft you can use a bit of string with a weight at the end and a ruler to find out the set back/forward. Then see how the front end feels and if you need to change it from what you had on the Kepler.
Changing my saddle height away from my fitted numbers is what gave me ITB syndrome for like 8 months.
Easy riding as pain allows should helps recovery a bit. Shouldn't take long to be back to normal :)