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@dancing james
it is amazing how a tiny change to the bike can have so many potential consequences
you may find that your saddle height needs to be adjusted a little as the position of your foot in cleated shoes vs trainers and clips relative to the pedal axel may be different
also the cleat on the shoe may need some tweaking
additionally it sounds like you have now changed your pedaling technique (pulling up more) which will also have put a different load on your knees
do you stretch your quads after riding? if you are now pulling up more your quads will be tightening up and thus pulling more on your knee cap as well