You had a 4 wheel alignment done right? Which is what one should do with a vehicle like ours that has 4 wheel independent suspension. You replaced 2 tires because they were worn and you put the new ones on the rear right? Which is what is recommended on a vehicle like ours that has front wheel drive. All of that all sounds about right.
The only thing is that the alignment was not done on some sort of measuring system, if I understood you correctly. That does not sound right. It seems like a very good alignment place would have a very good alignment system.
Do you think maybe you feel the new tires with brand new tread catching the irregularities in the road surface because they are brand new and have new tread?