It should be pretty easy really - basically, you need to change your assignments over to the new partition first, then execute the new startup-sequence. You can use a simplified startup-sequence on your default partition (3.1) which launches the original 3.1 script (which is renamed) if the version returned isn't 3.9. Something like this should work, though I haven't tested it:
Code:
Version 45 ; Is this a 3.9 ROM?
If WARN ; Nope
Execute S:Startup-sequence-3.1
Else ; Yep
; Reset assigns for 3.9 partition
Assign SYS: DH2:
Assign C: SYS:C
Assign S: SYS:S
Assign L: SYS:L
Assign LIBS: SYS:Libs
Assign DEVS: SYS:Devs
Assign FONTS: SYS:Fonts
Assign ENVARC: SYS:Prefs/Env-Archive
; Now launch 3.9 startup sequence
Execute SYS:S/Startup-sequence
EndIf
EndCLI
The AmigaDOS manual has a good reference for the various Shell commands. There's an online version for OS4
here, though most commands are the same so it's still mostly relevant. Don't forget to back up your existing scripts just in case!