I’m refurbishing my middle school computer, a Macintosh Performa 635CD
Cool. Eventually one the best 68k machine of all.
Will it hurt the chip?
If applied correctly not. Any increased cooling is welcome. Keep in mind that any heat spreader is at first an additional insulation, so its relative dissapation has to be higher than that.
It it is always a good idea to keep temperature down to increase longevity of chips. While the 040 isn't as sensitive as faster CPUs. Its 6..10 Watt dissapation at 33 MHz may seam low, it does need cooling in every situation (well, maybe except mounted in a fridge :). For basic 6 Watt at room temperature (25 C) Motorola recommends an airflow of 250 LFM or better. That's why Apple placed a fan right above the CPU. These 250 LFM are just enough to keep it within design limit, not optimal. So adding a heat sink will improve cooling considerable due the larger surface contact between airflow and heat sink.
Now, removed heat is a function of temperature difference, surface size and coolant (air) flow. By just adding a heat sink you improve only surface size. It might be a good idea to add on the air flow as well. So why not adding a CPU fan as well?
Some old PC might be a good source for both.
Applying paste. Assuming it’s ok to directly apply,
Yes, and Motorola recommends it for not glued on heat sinks.
I’ve looked at probably a dozen youtube vids
Don't let them scare you. Everything modern plays in a complete different league than a 040. If at all, you need to look at videos explaining the use with 486 and early Pentium - and I mean early real early.
yet spreading it with a card or something is dangerous because it will sort of roll over the edge of the chip onto the board and cause damage.
Spreading with a straight object is not problem - and it's up to you to do it without making a mess.
I usually put a little drop on, slightly out of center and used a razor blade to distribute it a bit. After that I put on the heat sink and turned it a bit sideways to really spread it.
The whole point is to use as little as possible. The whole schmeer isn't meant to be anywhere between the heat sink and the packaging at all. It's only the lesser of two evils meant to fill only those areas were both parts don't align perfect as it's thermal conductivity is better than air.
There are chipset heatsinks with thermal paste pads [...] but everything I’ve read about those says they’re junk.
No, they are good. In fact, most(default) cooler use them nowadays. They did win the race because of simplicity in setup. But as with all parts of the heat dissapation system, they are meant for a certain setup. Just picking a random one and using it may not be the best choice.
It may be a good idea to have a read of the 68040 User Manual section 11.8 Thermal Characteristics and 11.9 Thermal Management. They describe in great detail the various parameters. Section 11.9 not only discus various levels of cooling, but as well give tables for quick reference.
Looking at the tables adding a heat sink plus forced air (a reasonable sized fan) whill give quite great results and keep the gate temperature down.
As said, I belive the 630 to be one the greatest 68k Mac of all (*1). It can bring you quite close to the top performance possible back then while still being a quite compact desktop computer. I got a 630 DOS on my workbench fo all things classic Mac and haven't found anything better. Depending on the mainboard it can hold up to 132 MiB of RAM - that's 4 MiB (the soldered on ones) more than the top of the line 840 AV (*2). Under classic OS 132 MiB is like infinite memory. At least I never managed to fill it.
The 630 can as well be fitted with a full 68040 to add an FPU and set to run at 40 MHz(!), again on par with the 840AV. Given, the disk system is a bit slower due using IDE, but as you already mentioned, it as well allows the use of a more modern Flash drive, flipping chart :)
I would suggest to have a look into which board is used in your machine (while trying to max out RAM) to see how to turn the clockspeed to 40 MHz. Usually all 040 will go along. While this is as well possible without, it should go hand in hand with adding a heat sink and CPU fan.
*1 - The best from today's view, might be the the LC 475 and its direct siblings. In RAM size and performance it's a 630 in a pizza case, missing the CD drive, but adding higher graphics resolution. Unlike the 630 it can still fit the IIe Card allowing it to double as a IIe as well.
*2 - Quadra 950 could do 256 MiB