Have the disk ][ drives been upgraded to use DB-19 cables? If not, you'll want to swap in a disk ][ controller card into slot 6 and flip the slot assigment from "Disk Port" to "Your Card". The only caveat to this, is if you then want to boot from a 3.5" disk, you'll need to hit control-reset, then do a PR#5, since the machine will not automatically scan down to slot 5 from slot 6. Either that, or go back into the Control Panel CDA and reset slot 6 to "Disk Port", which, alas, means that you won't be able to use 5.25" disks for that time period.
I'd probably move the SCSI card to slot 7, which is what the IIgs expects it to be in, hence the reason slot 7 is set to "Your Card" by default. For parallel printer usage, I wound up switching to a Grappler c/Mac/gs (aka Grappler 9-pin) interface with my old Stealth GS, when I was using the original //e's Epson MX-80 printer with it. Did allow B&W graphics printing with said printer, whereas the Epson APL board and the clone I'd used previously did not.
Color monitor-wise, you can use either the more common, but less aesthetically correct A2M6014, or you can use the AppleColor 100, which, yes, is very rare, but fits the //e case better. Both have the proper analog RGB input.
For GS/OS, either 5.0.x or 6.0.x would be better than 4.0. Since my Stealth GS was the barebones version when I had the upgrade done in the summer of '89, I was stuck using an early version of ProDOS 16. The version that used the Apple II Desktop (aka MouseDesk) version of the Finder. So, it first booted ProDOS 16 and loaded up a program selector, then loaded up ProDOS 8 to run the Finder. In early '92, I finally fixed the RAM issue and bought a GS-RAM Ultra card. Once I did that, I was finally able to use the GS/OS disks that I received with the upgrade kit and the A9M0106 floppy drive that I bought for the machine.