Numb parts suck! Cycling shoes are so weird- they tend to be awfully narrow and give a lot of folks problems. This may not be your problem specificly, but it's common. I have some shiny (yes they're silver) new Lakes for the great day I get cleared to ride again. They tend to be wider in the forefoot than most shoes, and on the trainer they are significantly better than the ole Diadoras. Too pointy a toe will be hell after those first ten miles; Your feet expand and move up in the shoe and the fit can be very different than in the store. You gotta wonder what shoe designers think woth those pointy toes. They don't fit most people, especially men.
So how did the cleat/ knee issue work out? Is it resolved? Something that can help enormously is an orthotic, and you can get some surprisingly good ones for cycling and skating called Peterson Powerbeds. Performance Bike used to have them or your shop can get them from Gita USA (the distributor for Giordana and Diadora). Cost about 30 bucks. Orthotics will improve the way your foot sits in the shoe and stabilize your heel if it tends to swing around. Knee trouble from an unstable calcaneus is an involved explanation, but it happens and a lot of cyclists use these guys and love them. Even my orthotocist, who makes my expensive custom screwed up legs orthotics was impressed. There fantastic for skates, too.
Just a thought. Sorry to overwhelm you with information. After all I've been through with knee trouble and the trouble it caused in my feet and hips I wouldn't wish a sore knee on my worst enemy. Best to correct it early.

Miss Liz