From the description it looks like faulty thermal control of the motherboard.
Also, it's not clear for me: did you applied just enough thermal paste or were generous with it?
Solutions I see right now are:
- Update BIOS of your new MB. Quite often that does the trick on both cpu running too hot and fan not working correctly.
- If you used a lot of thermal paste it's not good. Paste is not good thermal conductor, you should use as little as possible. In essence, it should fill micro-cracks and other imperfections ion the contact surfaces of both cpu and heatsink. If you did that already (use minimum amount of paste that is), no issue.
- Fan may have developed a fault. If #1 option is unsuccessful, check with other fan that is known to be working properly (just for tests, so it may be old one). But the cpu is mite too hot, so it may be it's just compensating for that.
- Are you sure you connected the fan to the cpu_fan connector? I know... But better to make sure. You have quite a lot of connectors there.
- Make sure you placed and locked the heatsink correctly.
I know most of what I wrote is really basic stuff, but please believe me, I made all of the errors above at one time or the other. If all that fails, it may be that new MB is faulty... I've seen that happen as well.
Windows not genuine is normal after MB replacement - you need to contact Microsoft on that. They will sort it out.
EDIT: afterthought - did you set up BIOS settings of new MB to default? Maybe it's overclocking the CPU on current settings?
This is a little like the bumble bee -- if it knew about aerodynamics it couldn't fly. You may be over-thinking this a little. Laptops are designed to be used. They include everything necessary to dissipate heat as long as you let them do the job. You should be able to set it on any solid surface, with some clearance so no vents are blocked, and do anything the laptop was designed to do.
This assumes you're using it in a typical work area that is at a temperature comfortable for people. If you're working in an unusually hot environment, you could think about augmenting its cooling ability.
The most important thing is keeping the the internal air flow good. That includes periodically cleaning out the vents, and getting dust off heat sinks and fans. If you use it in a dusty environment, you will need to do that more often than if it's used in a clean-room.
If the bottom of the laptop is solid
If the bottom of the laptop is solid and plastic, the surface material it sits on should make virtually no difference. Setting it on a laptop cooler would not affect much either. Raising it off the desk won't do anything but potentially make it unstable or stress the case.
If it has a metal case that's designed as part of the heat dissipation system, a laptop cooler or a solid metal desk would have little direct effect on instantaneous temperatures of the heat-sensitive components. However, they might, theoretically, provide a little extra margin if it runs hot for long periods (in the category of "shouldn't be necessary but couldn't hurt").
If the bottom of the laptop is vented
If the bottom of the laptop has air vents, the case should already be designed with the clearances it needs as long as it rests on a hard surface. There will typically be feet to provide some air flow space underneath. The surface material of the desk will make virtually no difference.
If there is an internal fan that exhausts out the bottom, raising it a little may make the fan more efficient. In this case, you would not want to put a cooling unit under it, since that would interfere with the fan.
If the bottom has only intake vents, raising it another fraction of an inch or using a cooling unit that blows toward the laptop "shouldn't be necessary but couldn't hurt".
The science explanation
I don't want to get too far off-topic for the site, but the gist of your heat question is this. If you were talking about a metal desk, the metal would conduct a lot of the heat away. A material like wood or MDF is an insulator, so not much heat will be dispersed. If you're comparing dead, trapped air to an MDF desktop, the affect of either insulator wouldn't make much difference to the laptop. If the air isn't trapped, there will be some turnover; if not a laptop fan pulling or pushing the air, then just thermal action and environmental motion. So an air gap would probably be theoretically better than MDF, even if the laptop has a solid bottom, although there might be no practical difference.
The trapped heat won't transfer back into the laptop, it just represents laptop heat that isn't being dissipated from the bottom surface. Just like if you bake food in an oven, the food will absorb heat from the oven. But it can't get hotter than the oven so that the food is heating the oven. Eventually, the food will reach the oven's temperature and the oven won't transfer any more of its heat to it.
All that aside, remember that the laptop was designed to operate in this way. It has either a solid bottom that is designed to sit on an insulating solid surface, or a vented bottom that contains provisions to ensure a gap for air flow. So the laptop case is already doing the heavy lifting on its own. It isn't so much a question of which option is better, as will either option make any difference?
Best Answer
It isn't very strange that speedfan can't detect your fan. It's probably incompatible with your chipset or fan controller. If speedfan could detect your fan and it was dead, you would get a reading of 0 RPM under its speed.
The heating problem is normal. If you haven't cleaned your fan until now, you should consider doing so as soon as possible. The insides of your laptop probably look like insides of a vacuum-cleaner right now. I've seen fans die because of dust. There are no standard laptop fans so if the fan did die or is near death, you may need to look for a spare part for your exact model. The fan could be several times more expensive than standard desktop fan.
The replacement itself should be pretty simple. Just access old fan, remove it and place new in its place. However problematic parts could be accessing the fan and obtaining new one.
Right now you should try to clean you old fan. If you could remove the keyboard, accessing fan shouldn't be more difficult. You should also get sole compressed air and clean the dust in heat dissipation system.