For the transfer:
http://www.nintendo.com/consumer/systems/wiiu/en_na/system_system_transfer.jsp
It gives instructions. It insists that both systems are connected to the same TV and both be connected to the internet. I believe both systems must be on.
Try follow the instructions again based on this webpage.
Since you have the steps of having the SD card dump already, with both systems connected and on, try running the system transfer channel again on both and seeing if you can somehow get it to work / resume.. I believe both have to be on so Nintendo can update both systems through the internet to reflect the transfer.
It also says both systems must have the same country setting
In the worst case, try send an e-mail to Nintendo to detail your current situation, where you have the data from the Wii transfer on the SD Card and it is not letting you transfer it to the Wii U. Perhaps they can give you good details on how to proceed at this point.
For the homebrew:
There is a save modification software that was made quite early on.
FE100-1.2b_fix
It gets you to dump all the keys from your Wii with a homebrew, at which point you can put them into the program and be able to modify saves and save them appropriately.
I would suggest getting the all the keys from your Wii (xyzzy homebrew).
At that point, I'm afraid I wouldn't know what to do..
I would suggest sending a message to someone on the wiibrew forum, or someone around team twiizers (maybe IRC) to tell them about your half-way transferred setup, and that you have your keys. They may be able to help you to take your files and transform them with your keys to a state that is restore-able..
I believe in the same fashion that having your keys can help to decrypt/encrypt savegames with the right tool (FE100), I would believe that having your keys can help to decrypt/encrypt your specific transfer files too. I wouldn't know what to do once you get your keys, but I'm sure they will help. You would have to ask wiibrew/team twiizers if they can assist in converting your files to a restore-able form..
If you made a bootmii nand backup before you started I would suggest trying to restore it to your Wii.