@FCL Linking to your other thread for context: I made a sangaboard V0.5 .
The image from the low cost module is lovely. For the high resolution one, am I correct that you now have a 40× lens designed for 160mm ‘tube length’. If so, have you reprinted the optics module for the finite conjugates objective? A finite conjugates objective on an optics module designed for an infinite conjugates objective will have a reduced working distance. That reduction could well be enough to make it less than the thickness pf a coverslip.
One thing that you could also try is to put marks on a plain slide using a permanent marker. Are you able to focus on that, when it is on the same side of the slide as the objective? If so, how big is the gap?