I think you will find using a TorVM template is an incorrect approach. The i2p network does not use standard ports. Basically, i2p is a closed network that (ideally) uses no exit nodes. I've been using i2p for some time and the following seems reasonable to me:
1. I use a dedicated AppVM based on the Debian template with Oracle Java 8 and the unlimited JCE policy for Oracle Java 8. Using Debian allows me to avoid the Fedora issue with ECDSA signatures (still unsupported out the box last I checked) and Unlimited JCE policy helps with enabling SSL in the i2p interface. *This version of Java is recommended by the Freenet Project, as well.*
2. You can use Tor Browser. You can disable vidalia at Tor Browser startup using a config file. I don't know how easily that will apply to Qubes and it's workings. If you do this. you can set the proxy settings to what i2p needs, there is a plugin in i2p to enable Tor. It is called Orchid, I think.
2a. Or, use FoxyProxy as an add-on with Tor Browser. There is a custom script if you do not know how to build one floating around reddit.
3. In the AppVM firewall, feel free to disable DNS requests. Make sure to forward your ports. BOTH TCP and UDP.
BTW, torrent software has to be i2p-aware to use the i2p net. Unless you use Vuze or an experimental Transmission client (that I believe is now quite old) you should stick to an i2p-only client.