Isn't the upside down-ness, likely to be nothing more than not every game is oriented the same way? That's why I usually put yoke switches into my Jamma cabs with the alternative obviously to be to physically rotate the monitor, but clearly that's not all that convenient to do if you swap games a lot. I'm not getting into the details of making a yoke switch when it's been stated that pulling roms is beyond the OPs skillset but if you search, I'm sure I probably posted how to do it at some point in the last 25 years. Just don't get it wrong.
"flakiness" / glitching with graphics could be a number of things: dodgy / old / dirty ribbon connectors / plugs / sockets, voltage drops (potentially related), purely timing or quality issues with bootlegs. And sometimes, just the way bootlegs are. Depends just how bad and glitchy of course! Sometimes it's best not to look too deeply at these things
