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Practically speaking, setting up a BOCHS emulator and using IDA Pro debugger is a pretty good way to go about this. Not sure but likely x64dbg can do this as well. The only way to debug this early in the boot process is with some sort of emulation unless your BIOS had some really special remote debugging features. Though in a VM it would seem possible I've never seen a good way to go about this. Even remote kernel debugging is of course too late for studying the MBR.
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