How long did you drive around with the bad waterpump?
A few reasons why it might be over heating -
1. System not bleed correctly.
2. Popped a HG while the waterpump went to shit.
3. Clutch for the clutch fan is bad.
4. Stock fans not working.
If you caught the waterpump before over heating the motor, then it's most likely air bubbles in the cooling system.
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