My 1994 Mazda 121, manual transmission, has started making a loud whirring noise from 2nd gear through to 5th (worse/louder in 2nd). There is no issue with transmission or engagement of gears, smooth changes, and no clutch issues. What could be causing this noise? It is constant through acceleration. Car has done 203K.

the starter motor on the engine cranks the engine fast.
or does not.
fuel never causes starter motor to fail (unless hydralocked)
car is in Australia or Europe. not USA 1.3L or 1.5L engine.
when you turn the key to run (from off)
the dash IP cluster lights up. and glows many lamps doing the lamp self test. does it?
then you turn the key to start (this is cranking) and the starter makes a loud noise cranking fast on any dead engine,
grrrrrrrrrrrrrrrgrrrrrrrrrrrrrrrrrrrr, (like grinding coffee)
the engine crank shaft even spins fast, (seen by looking)
if this fails cranking there are 6 causes (and tests)_
if engine fails to start but cranks fast there can be 50 causes.
and lots of tests using tools you do not have.
for sure old cars like this., things do fail.

tell what the starter does.
the M/T transmission cars can be push started.
in 2nd gear.

Go for the manual they are easier ti repair.

Sounds like it might be a transmission mount or engine mount faulty

It could a wheel bearing. See if the noise gets louder at higher speeds. If it does trying jiggling the steering wheel (in a safe manner) from left to right and see if the noise gets higher or lower. If it does then you have a front wheel bearing that is bad. If not then if could be a rear wheel bearing. If none of these apply to you then try checking your transmission fluid level and fluid condition. It is posible you could have an internal transmission issues. The fluid should be bright red. If brown or black I would consider taking it to a transmission shop to it further looked into.

check /change the trans fluid as a first step ,if not done so recently, if no better have the OBD codes read as may indicate a specific issue

check the drain plug magnet for metal bits . If any the box has to come out 4.th gear is straight shaft connection and 5 gear connects from the cluster shaft up to the out put shaft . On either side is a rear main bearing and from your description if that bearing is failed then the 4th gear syncro will not align properly and the gear for 5th will be out of alignment so the syncro to work will not work

Check your belts and pulleys. Belts should not be cracked and pulleys should turn freely with no noise.

Mine has a high pitched whistle at high rpms and I can't figure it out. But mines def not the tranny. I'm thinking it's a vacuum line somewhere. It's a 97 2.3l manual. The colder it is the louder...

that definitly sounds like plugs and wires

It's weird but it's the problem!!! There is a switch on the transmission near the selector, usually only affects 3rd gear!!! The switch is being distorted after repetitive battering with gear selection!!! I have experienced it and also read about it in australia on a Navara!!!