Physical space is actually a huge issue
Ah then I'd recommend keep the existing machine as the server (it sounds like it's serving you well hardware wise), and get a SFF machine for regular desktop use, be that a new build or a used office machine. The trick will be in migrating the server to Linux, and without endangering your data in the process.
Anything USB connected more likely to be flaky, but a good enterprise disk shelf and a HBA card would be rock solid (just noisy...)
Unfortunately my solution when I did a big data migration was to buy more (cheap) storage lol. Ultimately it was a cost vs. time/stress tradeoff.