Here are a couple of points to keep in mind.
The Drive is capable of pushing the fins well beyond horizontal as shown here.
Most hulls stop the fins way short of their potential limits. Depending on the boat, the masts will either slap the hull with the fin or the Drive will make contact on the side of the sprocket as highlighted in this next view:
In most cases you will find this to be your limit and will adjust your pedal settings to stop short of this point. This is the most common noise. It usually happens on one side or the other due to normal fin alignment, Drive alignment or leg length variations.
The current sprocket cogs are designed to eliminate chain skip that could occur in the older Stainless Drives. The fat center cog as can be seen here, is purposely a tight (press in) fit. This is to secure the chain during assembly and again keep it from skipping during operations.
If the fins are allowed to rise much past the horizontal position (depending on Drive wear. chain tension and hull limits), the chain can pop in and out of this master cog. This is very noticeable, but is not a defect nor does it cause any damage. Normally, either hull slap or your pedal adjustment should stop you short of this point.
So, as you're troubleshooting your various thunks, thwaps and thuds, keep these in mind.
All the aforementioned happens at the end of the stroke. In Eecher's case, it sounds a lot like Synovis' chain alignment problem, as it's happening near mid stroke under certain chain loads. A close inspection of the cog edges for chaffing may confirm if and where this is occurring. Just be conservative in where and how much you file.