So. You've copied potantially conflicting libraries onto the new VM, and I'm guessing this may create problems for you. As this is a fresh install, I'd suggest doing the following:
- Duplicate installed software:
dpkg --get-selections > packages.txt on the old system will give you a list of all packages installed on the old system.
- Copy this file to the new system, and run
sudo dpkg --set-selections < packages.txt
sudo apt-get dselect-upgrade to perform actual installation according to the list.
This should give you identical software on the two systems. When this is done, you can start copying user data. /home you can copy by creating a tar archive, or you can simply run
sudo rsync -avr oldhost:/home/ /home/ on the new host. This uses ssh to copy data. Repeat for other areas with user data. Databases is best copied using mysqldump.
Then add users as per the old system. If you're brave or have many users, you can simply copy the relevant portions of /etc/passwd and /etc/shadow (but DO NOT copy the system users, as they may have changed).
The next step is to start moving settings. This is a somewhat manual process; copying /etc/ in verbatim is likely to provide strange results. Copy what you actually need, and if software has changed major versions, re-implement it by looking at the old configuration.
Copying / like you've done has created a system where package db is inconsistent with what's actually installed and you have the risk of old, conflicting libraries and binaries.