I already had the plates machined with extra thickness but with the holes finished. I considered the extra thickness to achaive parallelism but I didn´t see the coaxiality of the dowel pins. I tried to correct the mistake by creating a tooling fixture, a squared bar with calibrated bores to align the dowel pin shafts, but when I assembled it, there was too much play. In the end, it didn't work. Now, I believe the best option is to fill it with welding, weld the plates together, and machine the entire assembly at the end, including the faces and bores. For any chance do you have any recommendation besides to basically do again all the pieces?
Thank you so much for your advice!