Whoah..I scanned the thread but there is no detailed description of an impact. So far, all evidence of prove are at least academic researches, which describe a theoretical attack vector.
IMHO: Nope, Nope, Nope. From a technical view it is quite unlikely. I see there only a paranoia and I have not enough time to explain why. (Question 5 shows clearly that you are not understanding the basics of hardware.) I'm out of this thread.
1: What is the sideffect of that kind of rootkit? 2: Some BIOS have an option to block the update routine under a user context 3: Some BIOS have an option to recover a bad bios. On the motherboard are two seperate chips. 4: Did you compare the bios dump with an original one? at least a high rate of equal parts should be visible. 5. YOu have got a willem programmer. There is no furher use of a bus pirate. In combination with flashrom, it does nothing else different.
In my opinion it is very unlikely that you are infected by a multi platform low level hardware malware. Otherwise you are a subject of interest of a secret service ...Do you?
You need to gain the privilegs to get out of SMM. Maybe the "Admin rights" under windows are enough, probably not. Use flashrom under linux or at least a dos enviroment via LiveCD.
I wonder why you try to update the Intel H81. Usually it is done by a microcode update packed into a regular BIOS Update. You should ask here for a modded bios. Otherwise you get easily a bricked motherboard. https://www.bios-mods.com/forum/
It is not so easy to program a flash in circuit. Usually you have got an Vcc line which is powering a bunch of devices. maybe you need to plugin in the power cord for this laptop and get a basic Vcc. if that does work, you have to check the Pin for WP. It is normally connected to the Vcc, so that it is constantly write protected.
There are some problems. -maybe In Circuit Programming is not possbile -> desolder the chip -Rom is fused
but the PIN 1 to 3 seems to be assigned to ICP(page 157), so we need to translate the pdf into something readable. And there should be something, how you can read or flash the rom. At page 127ff somehing is written about ISP.
I guess, the other chip with 8 pins is the driver for the speaker.
What do you get, if you dump the EEPROM from the 8051? Tried a dissam on that part of hex?
If the use Java Embedded, it could be there. But it is nothing like the common Java. It is more like c++ under arduino after cross compile. Some sort of heavy optimized assembler. (FYI: your SIM card in the mobile phone runs also a sort of java embedded)