You can in some instances edit the bigip.conf and bigip_base.conf file directly to alter small differences in syntax/VLANs/interfaces. However, there is enough stuff going on "behind the scenes" that it could get ugly if everything is not in place (this is particularly true if you upgrade to 9.4 but that doesn't apply here).
What might be easier would be to save the config on your 9.1.2 boxes (b config save /config.ucs), and then perform an upgrade to 9.3.1 on the other disk partition (the one that 9.1.2 is not booting from), and rolling forward the 9.1.2 config file during the upgrade. Then you will have a 9.3.1 config file that you can transfer directly to the new units.
Denny
Nimbostratus
