The laggy file transfers are definitely seen all over all these units as a result of that IDE->MicroSD controller.
@Mu0n, since you're going to be getting a scope analyzer (I unfortunately don't have the $ for a nice one so all I got is the cheapo one on eBay), can you check the true frequency rate of the clock on the SD card as you're testing? I am not skilled enough to know exactly what MicroSD uses for communication, but I did notice that it looked a lot like an SPI interface. If it is in-fact an SPI-like interface running, I bet you the speed will be controlled by how fast that clock line is going (a big duh, but hear me out). So, regardless of it being in 16-bit/32-bit, this or that, if the source clock speed to that MicroSD card never changes (because it's hard coded or controlled via other means (like some sort of internal divider), maybe?), it just ain't going to matter. We will be 100% limited by that link in the chain.
The reason I mention is because I am unsure how fast the device's SPI speeds can go up to, but I've worked with SPI based video units in the past that had a 20MHz rate limit on their SPI clock line, so maybe there is a similar limit being imposed here? Might be worth looking into how exactly that MicroSD card is interfacing with the SOM. Cause it certainly ain't an IDE line despite living on the IDE line.
I also did buy me a programming book on VxD Win9x driver programming a while back, but I'm not going to lie, it's pretty involved and not for the faint of heart (and here I thought I could learn anything if I put my mind to it), and not like I have access to the source code of this stuff anyways. I would gladly loan it to anyone who thinks their Win9x C++ skills are l33t enough to take a stab at it, alas. I'm not eager to run down that rabbit hole.
I also tried a bunch of various different disk options in one of those hidden Win98 menus, and it seems like, for what I tried, I wasn't seeing much change in anything. I welcome others to attempt to try the same, I was not the most thorough by any stretch.
Oh, and I guess I let my mom convince me to build another 4 units, just because she thinks the ones I made are worth way more than what I sold them for. I dunno, I'm not out to take advantage of anyone, but I took her advice and bought all the parts for another 4 units, and this time put it on a different credit card so I could track the expense a bit better. I will have to sell these at auction rates tho, just because of the time investment. New boards are ordered, new parts too, only had to sub 1 or 2 additional parts out (which was fairly easy to do so). BIOS chip had to get the -M/SN version, but seems like the same thing basically. The only main thing I had trouble with, again, is the 3.3 LDO, which I did kinda find a 1A (similar to Muon's actually I believe (or someone earlier in the thread)) that I'm sure will work, but also ordered the right one from China. Crystal chips ordered off same eBay supplier, as are SOMs + connectors from WDL (US distributor). Unfortunately again with the SST NAND Flash, that I have to manually disable, but luckily is only a single resistor (or just the whole NAND chip, take your pick).