I posted in this thread about rubber replacement a fairly detailed description of what these bumpers do and where they are on both the ELS and LPS drives. I figure silicone of some sort would be a perfect replacement material for them. You can probably use silicone beads if you can find them; the bumpers don't have to be perfectly cylindrical, just with dimensions in the ballpark of the originals. I'd like to find something made of silicone shaped roughly like a glue stick that I could cut to size.
The "parking brake" is Quantum's AIRLOCK armature. Its function is to prevent the head armature from moving out of the landing zone in the event the drive experiences shock. It utilizes the air current generated by the spinning platters to move the arm out of the way once the drive spins up, and it's spring-loaded to automatically deploy when the drive spins down. You'll notice that in older drives such as the LPS, the lower capacity versions have an odd black plastic platter on top. This is because the air currents required aren't generated without two platters. However, this problem was solved in the newer ELS drives: the single-platter drives have a wicked-looking attachment at the top of the spindle that generates enough air to move the AIRLOCK armature.
The head armature really don't have any torque so the slightest stickiness to any of the bumpers will keep it from moving. Your drives are probably sticking on the bumper underneath the platters (if you use an ELS drive), though if the AIRLOCK armature doesn't move once the platters are at full speed, there could be something unusual causing it to stick.
I don't know what they were thinking with the 3.5" CDROM. I've only ever seen maybe ten retail CDs in that format and I doubt any developers were terribly excited to accommodate another weird Apple decision, especially one so unnecessary. If they had moved a few things around internally (such as the IR module and using flip-down feet instead of the spring-loaded ones) they probably could've shoehorned a full-size CD drive in the 5300's case with only an extra cm or so of depth. But of course arbitrary and unreasonable management ruins everything, as usual.
As for the 3.5" MO, like every other Apple drive it would have been built by someone else and who would have then slapped on a sticker with an Apple logo. 98% chance it would have been a Fujitsu unit (like the ones VST and Logitec ultimately used), though at the time IBM also made MOs, and Olympus was a noted manufacturer of high-speed MOs, though both were mostly focused on desktop devices. I'm sure that if MOs were more popular in the States they would have brought it to market, but between the expense and poor availability of the disks outside of Japan, I guess they figured it wasn't worth the trouble. Or, perhaps they couldn't get a deal with Fujitsu to make the drives to Apple specifications.
What would also be interesting would be a collection of 3rd party expansion bay models that aren't a Zip drive. Apparently there were some internal power supplies built, but what else was actually available? I have a VST MO 230 (sadly dead) but that's the only other thing I've seen for these machines.
Oh yeah? I figure a good SD controller with one of those high-speed SD cards would surely outperform an average HD, especially if you're not spending a ton of money on a fast HD. Most of these machines have problems with drives and/or partitions exceeding 128GB anyway; I'd stick with a 32GB flash card and call it good.
These drives only have so much controller memory available and are not reprogrammable without specific commands being invoked; none of them could autonomously reprogram their local memory. On a lot of drives, especially in the late 80s/early '90s, the program data was stored on an EPROM and couldn't be changed anyway.
Anything modern with SMART typically keeps everything related to defect management (among other parameters) in a special reserved area on the drive's media. I would imagine older drives do the same, except perhaps on ancient MFM-era drives that have the defect list printed on the top of the drive. Even then the disk driver/file system often keeps a record of bad sectors (at least SilverLining would map and reallocate bad sectors at format time or on-demand as errors arose).
Typically with trial and error it's possible to switch controller boards among any drive within the same family (so, a Quantum Fireball TM with another TM, or a CX with another CX), whether it's SCSI or ATA, higher or lower capacity. It doesn't always work, especially if there were large revisions somewhere in the product's lifetime, but it does more often than not. Apparently the Fireball TM had a very poor reliability record in ATA guise but was fine with the SCSI controller (though honestly it was a lackluster drive regardless of interface); I have a couple of the 3.2GB variant on ATA that aren't recognized by any host computer that I'm keeping in case I get a bad SCSI version to swap boards.
Generally only consumer-class drives (Quantum Fireball, Seagate Medalist, some IBM DeskStars) were sold with the same HDA on either ATA or SCSI; the high-end HDAs were only ever sold as SCSI ("real" Seagate Barracuda or Cheetah, IBM UltraStar, Quantum Atlas), though you could swap boards between narrow, wide 68, and wide SCA versions.
A few more mentions of this hardware: https://www.fenestrated.net/mac/MacLC/index.html and the related discussion here, along with screenshots of a board like mine https://ancientelectronics.wordpress.com/2017/09/28/macintosh-lc/.