I have one deck that I have truly altered: The Sacred Circle
First, I took a black sharpie marker and blacked out the keywords on the minor arcana because they had nothing in common with how I read. You could see the different color of black on black, so I took a silver sharpie marker and wrote my own keywords and now you can't tell I blacked some out but you can tell I wrote my own.
Secondly, her major arcana didn't work at all for me. Some of the cards were just wrong, IMO, like the artwork on the Magician and Hierophant cards was reversed. And some had been renamed and the new names added nothing. I blacked out all the names on the majors with the black marker and waited until I had forgotten what they'd been called originally. I sold the book to Half Price Books so I couldn't even look them up. Then I took the silver marker and wrote my own names for the majors on whatever card worked for me.
My alterations changed it from a deck that would sit on the shelf and never, ever get used to a deck that I actually reach for now and then. I wouldn't read with it for a client because it looks a bit childish; it reminds me of something I would have done as a teenager, especially the way the silver handwriting looks against the black background. But it works for me now.
Having said that, I am done altering decks. The decks I have trimmed or altered have all gone down in value, not just in market value, but in use value. They look amateur so I don't use them for clients, so they have limited value to me.