Hi all, thanks for the input and advice so far.
@VapechiK, I took your advice and reset drivepool settings and configured my balance settings to more or less the same as before. Basically, I turn off everything but disk space equalizer (by % used) and prevent drive overfill, and leave the automatic balancing settings alone. I've since started rebalancing again, and it's been plodding along at 50-80MB/s for the last 20 mins. It would start at those speeds before dropping to 10-20MB/s in the past, so fingers crossed speeds stay high.
Regarding the drives reporting weird storage numbers, that's likely due to files that have been allotted disk space but aren't using that space yet, such as torrents and other files mid-download. Below is a pic of one such file. When considering all those files on a particular disk (often a lot, I tend to queue downloads all at once and drivepools puts them all on the same disk), it totals to more than the actual available disk space. Now that I'm expanding my pool it's not a huge deal, was only really a problem when all my drives were getting close to 95%+ full.
@Shane, I did additional tests on S3D1 and S2D1 including a closer look at what has been moved to the .poolpart folders by drivepool. When transferring many small files, performance was expectedly slow, 5-20MB/s depending on file size, while large files were around 200MB/s. When I took a look at what had been balanced to those drives however, it was all large media files (not a surprise as that's 95% of my pool) so I don't believe that's what's responsible for slow balancing performance. As noted above my performance is a bit better since resetting settings but I will revisit this with an update after a couple of days.
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On a side note, this balancing behaviour seems a bit sub-optimal to me, and I'm curious if y'all have any input. At present, basically all of my drives need to balance in some way, either by filling up or emptying. However, only one of the empty drives has any balacing activity, and it's only pulling data from one other drive in the pool. It would definitely balance faster if it were filling both of the empty drives at the same time from multiple drives that are full. Is this a logic or file system limitation? TIA!