You are doing two conversions as you indicated. One is a platform change and the other is a software version change. Both have some challenges but are minor.
the bigger one is the interface changes as the upgrade conversion utility doesn't handle platform differences. It simply is checking and transforming the configuration to V11 form.
For the interfaces, go into the bigip_base.conf files and edit it. The Viprion guests don't have the interface pieces other than the VLAN's, so remove the interface statements and the statemirror (better to set up HA after you have things going no the new platform). remove the tag statements in the vlan,
check the VLAN names for consistency and that the names are what you will be defining on the Viprion host.
as far as the configuration (bigip.conf). I suggest that if you use the LTM partitions, move everything into the Common partition. V11 changes the way that the config is stored and it also adds fully qualified references to objects with the partition as the path. The common partition is stored where you have always seen the bigip.conf in the /config. the other partitions are separated into their own bigip.conf files in a directory structure in /conf .
if you have iRules that reference objects, in particular pool names, they now include the path so a check of starts_with or equals needs to be changed/updated.
edit the source which is in /config/bigpipe folder, and run /usr/libexec/bigpip doal to reprocess the config files.
errors can be found by looking at /var/log/ltm
(all the above is in a F5 document -- but I don't recall which one it is).