My only other question is the bottom of the new fan (shown in leftmost above image posted by ranchmom5), where it would seat onto the CPU, has multiple tiny dots of what I would say are also thermal paste. Do I just leave those alone, apply the Arctic 5 to just the CPU and they will seat to each other once running?
Sharon: These "multiple tiny dots" (like shown on the left image here
- use "Enlarge" to better see it) is pre-applied thermal paste by IBM, so leave them as-is
, and don't touch them. Clean off the old thermal paste from the CPU (as explained by RBS above), mount the new fan whereby the pre-applied thermal paste will create the thermal contact between CPU and fan/heatsink. Assuming that this is a genuine IBM-part, the quality of the thermal paste is likely OK, so just store your Arctic Silver 5 for future projects!
Also RBS, you said the "thermal pad goes on top of the GPU after removing the protective foil" I do not see any protective foil, although there is the "pink sheet" - which from what I have read is not supposed to be removed. With the old fan (shown in rightmost above image posted by ranchmom5) assembly, there was not a gray thermal pad.
The protective foil mentioned by RBS would (if present) be on the thermal-rubber-pad side facing towards
the GPU. Your fan does not appear to have been delivered with such a protective foil. No problem.
The grey (thermal?) rubber-like pad, shown on the leftmost image you link to, is on the heatpipe side of the fan/heatpipe assembly, facing away from the CPU/GPU. This grey (thermal?) pad will therefore be positioned between the heatpipe and the keyboard. I have seen these grey upper-side (thermal?) pads on T43/p fans, but I don't recall having seen them on T42/p fans, so I well leave it to some more experienced ThinkPad'ers to comment whether to remove or keep this upper-side pad. Provided however that there is sufficient space between the fan/heatpipe assembly and the keyboard, I'd leave it in place... I guess it may/will sort of "engage" the metallic part of the keyboard in the cooling process, which is good!PS
: By a close inspection the two fan assemblies are not identical; notice that the innermost heatpipe "bends longer" around the fan itself on the new fan. As we know the old fan is indeed a true T42 long fan, so is the new fan perhaps a newer version of a T42/p long fan, or is it perhaps a T43/ long fan? I am unsure of the specific heatpipe-look of T42/p "long fans" against the same on T43/p "long fans". Not of any great importance, though, it just caught my eye!
Good luck, young lady!