I'm a hurtin' unit....

I went for my first longish ride in quite awhile today. A measly 32 miles of virtually flat paved trail. I went with my friend Albert who was pulling his son in his kiddie trailer and we kept a kinda slow pace 'cause we were BS'in and enjoying the scenery. It was fantastic.....Until my knees blew up about 12 miles into the ride.
I just don't know what to think of it. I'm a youngish 30 something guy with a physical job and I think I'm in pretty darn good shape. Maybe it was the bike...It was my first long ride on it so maybe I don't have the fit dialed in. I've been riding it almost daily around town for 2 months but I've never ridden it more than 2 miles at a time.
This really sucks. I'm gonna do some research and try to figure it out. Maybe I'll revise my fit based on what I find out or maybe I'll just build up my mileage a bit before my next ride...I was braking in my new VeloOrange saddle too which was interesting to say the least. It's more like it was breaking me in. Ouch! The knees eclipsed the seat pain so it wasn't bad after a while.

So hear is the bike that I rode...The pic is from the mock up stage. It looks a bit different now.
My Peugeot 650b conversion: