When you got new pedals and shoes, your stack height also likely changed, meaning you should probably lower your saddle.

If I read your post correctly, you got fitted on the bike with flat pedals and cages and I'm guessing sneakers of some sort. By getting cycling shoes and pedals, you have altered your fit and stack.

The stack is essentially the distance from the bottom of your foot to the pedal spindle. Different shoes and pedals produce different stack heights. Flat pedals with cages and sneakers tend to be thicker and have a much larger stack than cycling pedals and shoes.

You likely need to lower your saddle some. That could fix some of your problems, as you likely are stretching to reach the pedals now.