1. I got files cIOS249[56]-v21d2x3.wad and cIOS250[57]-v21d2x3.wad to be installed as cIOS, but I was wondering if these are beta versions or not. Are they?
As davebaol already said, they're not beta. Dave and I coordinated the release of d2x v3 final to coincide with this ModMii update
2. In step 4, when all the WADs in the wad folder are selected to be installed, I wonder if for example my system menu update to 4.1 will be the first to be installed... Or the order by which these WADs are installed don't matter? Or does MMM know which order of installation to use? I never used batch installation of WADs, that's why I'm wondering...
All that matters is the the system menu IOS (IOS60 in your case) is installed before the system menu. And MMM installs the WADs in alphabetical order, so all the IOSs install before the System menu because "I" comes before "S" (In the 4.4.2 update I had ModMii rename all the system menu wads so they started with "S" instead of a number for specifically this reason)
3. In step 5, what version of Priiloader is installed and what hacks.ini file is copied over the SD card?
I've had some freezes on another Wii before when Priiloader was upgraded last time because of hacks.ini file, so now I'm always a bit concerned when it comes this.
v0.4 is installed, its the last stable version of priiloader that uses the older and much much safer installer. The hacks.ini file is a universal one (ie. it includes all the available hacks for all the system menu versions), it was first made by da_letter_a and then later modified by myself. It's been used/tested extensively so u have nothing to worry about
4. In step 6, what is the purpose/advantage of re-installing HBC to run over IOS58 (in case it isn't already)?
The HBC will benefit from USB2 speeds if it is running on IOS58. Note that even if you're HBC isn't using IOS58, u will still have USB2 speeds via cIOSs when running games off a USB hard drive. Also note that many apps with "no_ios_reload" in its meta.xml are built assuming your HBC is running off of IOS58... that's not to say it won't work off of other IOSs, but those apps will likely behave more like their authors intended when running off of IOS58.
I hope this helps!