There are a few problems here, fortunately most are relatively easy to fix.
Regarding the clunking - it is usually due to a bolt not being tightened properly (either from perch to top-hat, or hub to base), or from the spring not being seated properly between the top and bottom perches. Take the weight off of a corner and take a look.
There's also a chance that the height adjustment collars are not locked down properly. Again, take the weight off and get in their with your spanner wrench to check the torque on the adjustment rings.
There's yet another chance that these coil-overs clunk, period. When offering performance gains in suspension, there are few products that do not bring compromises (increased NVH, "clunking", rattling, etc) of some sort.
NOTE:
This clunking may in fact be "normal" with this product. Have you called the manufacturer to ask if increased noise is expected?
As far as the bolt on the top hat (one of the three that hold the top hat to the top of the fender tower?) It's not easy to replace. And it's a two-fold question.
a) Do you have camber plates installed? If so, you'll probably have to return it to the product manufacturer for repair/replacement.
b) Are you utilizing the stock (or even the Group N) Subaru top hats? If so, go buy a replacement top hat. You can often find take offs at places like NASIOC for a song.
Either way, you're going to have to remove the strut/spring assembly at that corner, disassemble and replace the top hat/camber plate, reverse and reinstall. Unfortunately, unless you've got a good selection of metric studs and the proper press to remove and reinstall them, you're going to be replacing the top hat/camber plate.
Those three bolts are meant to be torqued to somewhere around
14 ft-lbs. Suffice it to say - that's
reeeely gentle.
Hope the noise demons are easily exercised with your car.