For your axle bowing problem I think I would try adding the spacers under the frame support like you mentioned. You could start with washers until you got the right spacing and just see if that straightens the axles out and allows them to spin freely. If it does then make some permanent spacers out of some flat stock that is the correct thickness and make them the entire length of your frame supports. Drill out the holes and that should make for some solid supports.
For your center support problem, you could still leave those plates there and put another identical plate underneath it the thickness that you needed so you don't have to cut those off.
For your center support problem, you could still leave those plates there and put another identical plate underneath it the thickness that you needed so you don't have to cut those off.

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