Thoroughly clean the northbridge heatsink. After removing the old thermal paste on the occluding surface clean the fins. First use pressurised air. Then use a dinner knife with lint-free cloth soaked in isopropanol to clean each of the spaces between the fins.

Open the latch on the processor cradle to clean around the CPU chip. Don't remove the CPU chip: An unnecessary risk. There is nothing under the chip that needs cleaning, and many things easily broken.

If you are upgrading the chips, of course, you need to life out the old chip and replace it with the new chip at this time. However, upgrades to more powerful chips are not justified unless you are already using your Mac Pro close to its operational limit. Read the document "Upgrade Tips" to find out when and when not to upgrade.

Be aware that upgrading the chips in some machines will require Boot BIOS upgrade as well.