Hi AmigaMance
i think that we have (more or less and in different way) already answered to your question.
There aren't absolute bahaviours in such overheating situations. Usually CPU overheating, could freeze, crash even burn you CPU (but this is not your case, seen that you have already cooled it)
Then there are:
ICs regulators (2), the ram controller (those CY7C37)
The setup suggested by x56h34 its quite OK . . .but NOT remove the original 30x30 mm fan . . . .that is not there only to collect dust! ;-)
If you don't like the P5 solution, go for a separated heatsinks for the above mentioned components. (with a fan on PPC and on the 040)
At a side note, i've recently read an interesting article about hi quality and safe thermal glueing.
To avoid that the thermal adhesive, will broke the CPU if you need to remove it, its enough to mix the thermal glue with the thermal compound (in 1:1 rate).
You will need i'e Artic Silver adhesive and Artic Silver compound mixed at 50%.
Will be more easy to remove it (and Artic Silver is a very, very good product).
Last suggestion: check carefully that the heat of the components, is fully transfered to the heatsink (sometimes the haetsink "seems" cool only because, the thermal compound is applyed in a wrong way).
An easy way to check this is . . . run for about 30 seconds the system with the fan switched OFF.
The heatsink MUST rise the themperature rather quickly . . if not, there is something wrong on the heatsink installation.
If the heatsink will go warm quickly, you are OK . . . try it for no more than 1 minute or so and the shut down :-)