I'm not saying its inevitable, but its a pretty good chance. Keep an ear on it. If it gives ANY indication, STOP DRIVING IT IMMEDIATELY. You probably haven't done any damage yet. You MUST do the bearings, don't fret, its much easier than it sounds, below is a quick description of the FASTEST way to yank a complete motor and trans. You will get dirty and don't bother cleaning anything unless you have to (like the oil pan and block interface) It is a good idea to clean the whole oil pan its just easier that way.
1. disconnect the harness at the ECU push it through the fire wall, lay it on the motor.
2. Unbolt the driveshaft at the carrier bearing (mark it first). Use a bent up hangar to wrap through the u-joint and around the stickshift tower to keep the drive shaft in.
3. Unbolt the clutch slave,
4. Pull the stickshift,
5. Hang the power steering on the fender,
6. Unbolt the exhaust at the cross member,
7. Disconnect all the IC plumbing.
8. Drain and yank the radiator
9. Disconnect the hood struts to get it to open up farther.
10. Disconnect Throttle cable and Cruise Control cables.
11. Pull the motor and trans at the same time.
Rent a cherry picker, yank the motor keep it up high pull the oil pan (clean it inside and out) and swap all the bearings (less than $130).
replace the bearings (make sure your hands are clean for the whole job)
Rod bearings are easy.
Mains: remove each cap one at a time lube the new bearing put it on the crank rotate it around and rotate the new bearing into place and remove the old rotated out bearing. Install the opposite new one in the main cap and reinstall it. Now do this 6 more times. Make sure to do the Thrusts at the same time on #4 I think.
Now reverse steps 11-1. This is the quickest way I know to swap a MKIII motor.
Its not fun, but not worth getting rid of, You could do have it out, bearings installed, and set back in the car, in one day and Sunday take your time hooking it all back up. The whole thing done in one weekend.
Get a few qualified friends and show them a detailed list of the tasks and you could probably be done faster.
DONT GIVE UP!!!