I found that simply rehacking your wii will not work (I've been at this for a few hours now). The 4.3 update replaces IOS 222/223 (usb 2.0 support) and 249/250 (iso emulation/loader support) with stubs. It also updates almost every other official IOS, including 15 and 36, overwriting the fakesign bug.
If you simply delete IOS stub 249 with DOPMii and reinstall cIOS 249, skyward sword will still prompt you to update to 4.3 again, undoing the mod.
Now, the obvious solution to this would be to bypass the official 4.3 installer and reinstall cIOS 249, except Skyward Sword itself appears to actually check that 4.3 is installed again after the "System Update" has run, and crashes to the System Menu if all the IOSs aren't up to date. At least, I could not find a way (with either preloader or USB Loader GX) to get it to run with any of the 4.3 IOSs altered.
Anyway, the solution is simply to install cIOS 249, but in the slot of 248 so it doesn't get replaced with the nintendo stub (this is kind of fail on nintendos part, what did they think we were going to do?)
I used this to install cIOS 249 into slot 248:
d2x cIOS v7 Installer v3.1
http://www.mediafire...wy4dvdyben3fj03
Just select the latest version of the cIOS, use IOS 56 as a base, and install it in slot 248 instead of 249. - EDIT as per Cyan's suggestion
Or go here:
http://gwht.wikidot.com/d2x and install cIOS 247 and cIOS 248 if you want greater flexibility.
Then, you should be able to configure USB Loader GX to use IOS slot 248 instead of IOS slot 249, and you're good to go.
Also, if you need cIOS 222 for any reason, that can be installed in slot 202 without issues.
The latest DOPMii (14.5), doesn't require trucha to gain NAND access (it uses AHBPROT), so you can use it to temporarily downgrade/patch IOS 36 if other homebrew needs it. (this is why your wad managers are crashing, they need the fakesign bug)
EDIT: - Correction, like Cyan said, cIOS 236 should be installed to get around this issue (cIOS 236 is simply IOS 36 copied and modified with the trucha and some other functionality added. You probably shouldn't touch IOS36 once the system has been updated, although I did and it didn't cause any harm)
And the reason your wiimote was crashing was because USB Loader was trying to load cIOS 249 when it had already been replaced by a stub, and the system was simply crashing (just in case you were wondering)
Hope this helps!