If it's like my JVC AV-32320 you can get into the service menu by pressing the sleep button till it cycles through back to zero, and then pressing the "video status" and "display" buttons at the same time. There are some settings in there that will greatly help the image warping on your screen, it is very noticeable in mega man when the screen shifts vertically. There should be one that adjusts the top section, bottom section, and an overall vertical linearity control.
The bigger the screen is the harder it is to get the geometry under control, but you should be able to make a big improvement by just fiddling with those 3 controls and moving megaman up and down a ladder and watching the screen shift. RPGs with top-down overworlds are good to test this as well if you don't have 240p test suite. You could probably load 240p test suite on the SD card going into your Analogue NT mini, but if not there are a few other methods (I have it on a CD-R I use with my Sega CD).