It only can run after that thread completes (and then waits to
get rescheduled at a later time.

I know.  That's how my threaded app works.
So I don't understand why you bother about "real" threads at all. some 50 Lines of C code will "schedule" your "threads" one after the other as part of a single application/process, all running on the same stack, without Linux interfering at all. (That is what my PicoOS does.) You only need Linux's help with the interrupts. Here you need to write device drivers (or use UIO which I don't know anything at all about), which set some bits (e.g. in a memory region the user process accesses via an mmaped file. An example for this is in the NIOSWiki).

-Michael
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