Are BoingBag39-1.lha and BoingBag39-2.lha the only official ones then?
Yes.
What was the problem with BoingBag2? Should I skip it and only use the OS3.9BB2 after installing BoinBag1 or does OS3.9BB2 fix the BoingBag2 problems?
Like I said, the problem *might* be (and might be not) with the AmigaOS ROM update included with official BoingBag2. The installation procedure informs you about this and lets you decide whether to install it or not. I recommend to install it. If it won't work, simply rename the file like I suggested. The OS39BB2-patches.lha archive doesn't address this issue. It patches other files of official BB1 and BB2.