CPU Hot on startup!!! Bad CPU or bad motherboard???

If the sensors don't agree it's probably just a firmware issue.

A quick look on Asus' website shows that for your motherboard, full support for the i7-4790k was added with firmware revision 1008 with the latest revision being 1304. Calibration of the digital thermal sensor is a job for the firmware, so erroneous temperature readings on unsupported CPUs are no surprise. Update to the latest revision and see if that fixes the issue.

EDIT: wrong CPU model

I had originally wrote i7-4930K instead of i7-4790K. I corrected that in my edit.

As for that temperature problem, make sure that the heat sink is firmly attached. Intel's CPU packages are designed to take a lot of force, don't worry about breaking it. Make sure that all of the mounting screws are firmly attached.

If that doesn't address it, it may just genuinely be a borked sensor, especially if the temperature doesn't fluctuate a little bit or there's a huge difference between the CPU socket and Mainboard sensor readings. It's normal for the socket area to be hot to the touch. This is emphasized at startup before power saving states are enabled. 88 degrees at startup is extremely abnormal and would be a first degree burn level of hot so you may have to put yourself in some minor danger to determine if it is actually running that hot. Touch it carefully, if it is burning hot, something is wrong, if it is just really warm, it's fine. If it's not definitive, side with the lesser of the readings and proceed as normal.

Install an operating system and run HWInfo64, this will present all of the sensor readings including the digital thermal sensors (DTS) on the CPU die itself as well as the thermal sensors installed in the motherboard. The system firmware generally doesn't show all of the sensors together for comparison, Asus has a habit of omitting the DTS readings and presenting the readings from the motherboard's thermometers. The DTS on the CPU die are embedded directly below the heat generating components. Calibration isn't always the greatest but they should register the hottest. If the socket temperature (often presented as the CPU temperature) is displayed as being much hotter than the DTS temperature, something is wrong with the sensor itself. I've seen this happen before.

I'm having a hard time visualizing the damage. Can you post a picture of it please?

UPDATE: This is a long shot, as I don't know if you still have a working cooling assembly, but could you tell me what the reported CPU voltage is?

I don't have any Haswell microprocesors to check against but that seems extremely low. 0.7 volts is what I would expect while it is in a low power state. I'd ask you to test it under load conditions but if it's burning up already I'd rather not risk damaging your PC.

I'm at a total loss as to why this is happening. Either something incredibly obvious is happening and it's being overlooked, or something is seriously broken.

Did you purchase all of these products from the same place?

My observation from that picture is that the thermal paste does not appear to be melted at all. This would explain the ridiculously high temperature. The heat sink was not mounted correctly or firmly enough. Alternatively, the CPU wasn't generating enough heat to melt the thermal paste. This could mean that something else is generating the heat but that would clash with the HWInfo64 temperature measurements and there's enough material in there that the heat should have transferred to the heatsink by pure convection. This is extremely puzzling. As I mentioned previously, I don't have a Haswell CPU to reference so I'm just taking educated guesses here. In any case, since you have a Corsair h90, lets work with that for a bit.

Here's what I want you to do.

I want you to disassemble your PC entirely. I want you to take everything apart and spread it nicely over a working area. I want you to attach the h90 to the power supply outside of the case with nothing else attached. Just the h90 pump. No motherboard, no hard disks, no fans, nothing. Then, I want you to take a paperclip and jumpstart the PSU, this will allow you to test the h90 for proper operation. To jumpstart the PSU, take the 20/24 pin connector and short the Green wire to any black wire; there's a black wire right beside it that is easy to access. Don't worry about shocking yourself or anything, just be careful not to short any other wires after those two have been shorted.

Once the PSU is jumpstarted the h90 pump should start up. If it's operating properly, you should feel it humming slightly and may hear fluid moving around inside. If everything is okay with the pump, move on.

Next, I want you to breadboard the PC. Find a clean, non conductive surface. A chunk of cardboard will work nicely. Place the motherboard on the cardboard, insert the CPU, attach the cooler (along with fresh Arctic Silver 5), and connect the power connectors. Do not attach anything else. No hard disks or GPUs. Then, attach a display to the IGP and power it on.

If the temperature problems persist despite the breadboarding make sure that you followed the cooler mounting guide correctly. Many cooler kits come with a variety of mounting hardware for different sockets. It's possible that you may have used standoffs that are too long which may result in the heat sink making poor contact with the CPU's heat spreader. If everything looks kosher, RMA the motherboard and CPU to Newegg as I don't think that there's much more that I can do without seeing it myself.

I always enjoy trying to tackle the tough problems. Thanks for the appreciation and good luck with the RMA!

I didn't think that there was anything wrong with the h90 seeing as you tested it with the stock cooler as well but I just wanted to be sure.

In their defence, 99% of the time bent pins are the fault of the consumer. I find it utterly amazing how many people fail to read basic instructions, just take a look at some of the posts on this forum to see what I mean. Newegg doesn't handle the board outside of the box so they themselves are more or less absolved of responsibility for bent pins. It's possible that another consumer did and repackaged it very carefully so as to appear that the box was never opened, this has happened before. It's also an easy go-to method of committing warranty fraud to cover up other damage and Newegg doesn't have the facilities to inspect or repair complicated damage; The board will be repaired by Asus either way. If you present Newegg with your assembly vidoes they may be willing to reassess it and escalate if need be.

Newegg is one of the most well known and most highly regarded retailers in the world.

I would advise against using a motherboard with bent pins. Those pins exist for a reason and while some of them may be unused in certain configurations, the overwhelming majority of them always serve a purpose.

It would depend on which pin/pins is/are bent.