How best to fit stuff together that needs to be enlarged & rotated?

Hello everyone,

I've run into the following problem recently: I wanted to compare scans I had done on two different scanners for their detail level and overall quality. The two machines were pretty evenly matched, without a closer look at fine details it wasn't possible to discern which one was better. So I cut out the same sample area from both scans and tried to overlay them, just to be able to compare the fine structures within the same image. That proved a lot harder than expected because they had been scanned at ever so slightly different angles and resolutions, which I had to compensate. Now, when you transform (= change in size) one image, its view is grainier than the real image quality (I suppose to save processing power), making it difficult to overlay it over a duplicate structure even if you lower transparency. But you don't want to transform more than once because each transformation means a small quality loss. So you try to get everything done in one transformation - both the rotating and the change in size.

Now, in the end I got my images matched pretty well, but it took me almost half an hour for two really small images that were already almost evenly matching to begin with. I wonder if I'm missing something here. Photoshop professionals are probably confronted with similar problems all the time and might have much easier solutions to this kind of problem. How about you?