The case fan *must* be an exhaust fan, and therefore must be at the rear of the case. If you use an intake fan, that will destroy the negative pressure in the case, which in turn destroys CD drives. The CD drives can only get ventilation by means of the negative pressure inside the case.

When you check that fans are running, be sure they are running well instead of running very slowly. Sometimes the lubrication fails and causes the fan to run at 1/3 or 1/4 normal speed. To re-lubricate a fan, peel the label and inject a couple drops of thin machine oil, preferably silicone type. This won't last, so only do this if you don't have any new ones handy. The fact that you get good cooling with the case open, sort of points to the power supply fan.

The quantum change in heating could also happen if the core voltage somehow got raised. You can measure the core voltage by probing with a voltmeter on the solid metal tabs of the power transistors in the regulator circuit. Be careful not to touch more than one thing at a time with the probe. If that voltage is too high, maybe clearing the CMOS would fix it.

If the regulator is misbehaving, look for leaking capacitors. You can recognize them by the bulged-up top.

To get more ventilation, I leave an empty hole where the second floppy would go if you had one. This also obviates any need for a hard drive fan because the hard drive can be located near that front opening.