No, psxtoo1 is only for playstation games, you dump unprotected pc games the same way, raw like you would a playstation game. How I dump games is I first dump it once with one drive then again with the other. I check the checksums if they don't match I run the first image through cdmage and copy the error log to a notepad (*Do not use the repair feature*) then I run the second image through cdmage and compare the difference, now because they both don't have the same checksums there are errors in one image that the other don't have so what I do is have the errors display in the error log, hit Ctrl + Alt + I and pops up a window to import sectors, click radio button that says "Import sectors in the error log" use the image that don't have those errors and repair it like that.
Have you redumped 3 and 4 again with a second drive, did the checksums match? If they don't match try out my cdmage method it could be non-mastering errors that are giving you different checksums from the db one. (*I don't know if there is any mastering errors or not as I am not familiar with that dump.*)
I will also add I notice a drive can make the same error at the same sector and it's not a mastering error which adds even more weight to using two drives as the checksum matched, I dumped it with a second drive and that error wasn't present and repair like described above.
Three years and still going strong.