Sounds a good ride and I gather it was Ian's favourite commandant at Penshurst that you met
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These twinges and aches sound a bit worrying, particularly as you've been going so well. If you haven't done anything to cause them that you know of then check your bike position and shoes thoroughly. Have you fitted new cleats? Make sure they are in the right place (generally centre of cleat over axle spindle on pedal when clipped in). Also check they are both straight so that they aren't causing one knee to point in or out when in their natural position in the pedal. Give the bike a once over to check that the saddle hasn't slipped a little bit - it is amazing how little it has to slip before it can start to cause aches and pains.