I hope you find the root cause of the clunk soon.
The best finding would be just what you suggest, tighten the EBB bolts up a bit to stop it. If the EBB can wobble rather than slide sideways in the bottom bracket shell then it may be that a new EBB is in order.
There are quite a few other things which can come loose around that area, any or all of which could be contributing to a clunk - loose crank, loose pedal, loose chainring bolt(s) and a worn bottom bracket.
I still also get the notchy change up into 10 sometimes. I asked SJS about it after the first 300 miles - I was getting the notchy change up into gears 3, 5, 10 and 12 on a repeatable basis. I also had a couple of occasions when the gear slipped before meshing. I was advised to change the oil a couple of times and put some more miles on to let the rohloff bed in.
I changed the oil at 300 and 600 miles and noticed an improvement each time in a reduction in the slips and notchy gear changes.
I am now at 1100 miles and still get the notchy change into 10 and 12 occasionally, but it is not repeatable. I don't change up into 3 and 5 very often to have noticed it there.
Something I noticed for the first time the other day when I was stationary chatting to other cyclists - I rocked back and forwards with some weight on the right pedal at the front I got a noticeable clunk/movement within the gears which felt like a loose crank but wasn't.
I have just checked this and it is noticeable in gears 3, 5, less so in 6 and 7. This repeats in the higher ratio with 10, 12, 13 and 14 but with less effect due to the higher gearing.
Do you have this happening in any gears when you rock back and forward with weight on the pedal?