Fistly I would check the gearbox oil level and grade are correct.
If a NA it will take 2.6 litres of GL3-4-5.
I have exactly the same problem but mine was down to the clutch being changed before I bought the car and when this is done on the MR2 the gearbox has to be drained and clearly the muppets who did the clutch didn't refill correctly, if at all, so mine was very low on oil.
The fact you are having trouble changing gear also suggests this could be related to low oil level.
Be warned the filler and drain plugs can become rounded if the correct socket is not used and difficult to get off.
A new pair are
£10 from Toyota.
As a hint alwatys take the filler plug off first as otherwise its a pain to find you can drain the gearbox but not fill it!!
I have recently refilled my gearbox and included some
"Forte" gearbox/diff oil treatment which is meant to quieten the gearbox/diff but to date I can't say I have experienced any difference, but I have only done about 60 miles and sometimes these things take time to
"bed in".
On the plus side I've done about 10,000 miles since the noise began and yes it has got worse but not a lot and it's not intolerable, but I do think I will need a new gearbox soon if the noise gets any worse.
Good luck
Geoff