If you choose your Wii U's Mii, your 3DS Mii will also change, but only in the way that it looks. Your Streetpass data will NOT change whatsoever (you can even choose to use a different Mii in Streetpass Mii Plaza, fun fact of the day). Nintendo is very secure in every way (as far as I know), so go ahead and change that thing! But, just in case, I'd back up or copy your 3DS's user Mii so it doesn't get overwritten (if you want).
First off, in regards to your end question: No. The HD format for external devices on the Wii U is closed and proprietary, and each drive has the hardware ID for it's home system as part of the encryption so it will not work on a second Wii U without reformatting as of the last time I checked. This would require a hack which is beyond the scope of this website to cover.
As for confirming and commenting on the migration process, having just done this myself I can verify much of what you said. But it is extremely nerve wracking and the Nintendo associates I spoke with indicated that they are working on a way to improve the process in the future.
My situation was all of the family members in my household had NNIDs setup on a Wii U and those NNIDs had been associated with the Club Nintendo accounts which were apart of a Family account. Only the main account on the old system had made any purchases but the other accounts had extensive individual save data for games.
I spoke with several Nintendo support people about this and it seemed that the only ones that really had a grasp on this process where the M-F / 9-5 U.S. based support staff working out of their primary call center. Anyone else I reached that was a remote worker or over seas and dependent on the support scripts usually didn't seem to comprehend what I wanted done.
Anyways, with the right people handling it, the request is a "back-office, profile migration" and you have to make sure they specify in the notes that this is for a single profile. Not the whole system. Also make sure you have all of the NNIDs, Club IDs, e-mail address associated with IDs, and possibly be able to confirm recent purchases (on both the account you're moving and the primary account on the old system) as well the machine serial numbers in front of you when you make the call.
The only thing that get's re-homed/transferred is the NNID to the new hardware. All DLC or full games purchased by the transferred NNID become unlicensed and none of the other players in theory can not launch them anymore so those downloads will need deleted and/or repurchased by another user. The moved NNID will need to re-download all content to the new system.
Note, one support person I spoke with did tell me that there is the potential for a manual file extraction/move process on save game data as the techs can actually walk the file system on your Wii U while you have it online and turned on. In theory you could have both systems on and a support tech could move the files between the systems remotely. Unfortunately I was never able to get this particular support guy back on the phone to try this, but this does indicate that it is possible. I was told by this person that you could not simply do a USB transfer as save data for users are bundled into a save data resource bundle on the system and there is no way for the user to separate it out, also some save data is bound to the system's hardware ID and part of the support person moving the data is rebinding it to the new hardware.
The net result is my one child now has his Wii U with his ID on it. The original system has all of the other IDs. Also for some reason his ID still shows on the old system and did not deactivate. None of us have had the guts to try launching the profile as we don't want to screw anything up. Also, whatever you do, do not use the DELETE ID function as it will not only delete the ID from the system it will also kill the NNID account and all purchases ACROSS ALL ASSOCIATED SYSTEMS... yes, you may screw your 3DS up. Do don't do it.
The process is horrible. Absolutely horrible, and if you're going to do it, you need to make sure you have someone who knows exactly what you want done and annotates it EXACTLY in the back-office request. You should also make sure they are on the phone with you every step of the way as much as possible.
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Yeppers, as long as the folder containing the data to inject has been renamed to the correct user id (x000000x) this works flawlessly. I'm assuming this works by forcing the game's legit code to sign the save data to avoid hash mis-match? As O.P. stated, a direct copy using "SaveMii" for example, will result system hang and make it difficult to tear out the improperly signed data(I ended up using "FTPiiU_Everywhere" to manually delete the broken saves). As always: be careful a happy modding :-)