Saddle, that's a hard one to recommand, the most comfy saddle to me (Selle Italia SLR) could be the worst for someone else. It can take some time, trial and error to find the right saddle. Now I know just looking at a saddle's shape if I'll be able to endure it, I don't like saddles that are too round looking from the back and side... But we all have different butt shapes, sit bones width and 'natural padding' thickness...
I'll let someone else chime in for the pedals, I only use the cheapest non-clipless pedals I found on my commuter and I don't think highly of them, I don't even know what brand they are.
Michelin city tires are not bad at all. I have a pair of Michelin Transworld City and they have been going for years, probably the longest lasting tires I have had. In those years, I think I flatted once, rolling on a big nail that would probably have punctured any tire... They're not the same as the Pilot but I would expect them to be quite good too.
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