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I have no experience using ME Cleaning tools, I do it manually, so I can’t comment on any of that.
Please upload your source BIOS/ME and then your mod ME FW by itself, all in one zip, and I will fix ME for you. Or, if you want to do same as I would, extract ME FW from source BIOS, open in hex, select all and note the size.
Open mod ME in hex editor, cut off any padding at end (Or add FF to end if needed), until it matches stock ME FW size. If that fails, open stock ME FW file from the repo in hex, and make your mod ME FW that exact size.
Looks like you need to add padding to make it match 8D2000h length, you’re files cannot be the same size because 210000h is much smaller than 8D2000h
If that files, then you cannot flash in mod ME FW like this, you’ll have to insert into BIOS and flash with BIOS flash tools, or unlock the FD and flash the ME FW via FPT (only do this once your file is exact size of original ME FW region - 8D2000h)
If you have hardware flash programmer, then no need to waste time playing with any of this, dump your current BIOS contents, unlock the FD in that file, edit your ME (Extract, edit, pad out as needed, replace) then reprogram BIOS.
Yes, BIOS and ME can be joined if you dumped two chips, whichever contains the FD/ME region should be first, append the BIOS region at end of that chips contents. ME Clean tool should work on this as a whole, if not use FITc tool instead.
Upload your two dumps BIOS chips if you are not sure about how to append the BIOS files or can’t get ME Clean tool to work for you, I can do all this if you want. You are just disabling the ME FW via “Reserved” bit correct, or I mean that would work just as good for what you’re doing instead.
If you want help with me_cleaner, ask at the Issues section of the github repo. Our goal here is to mostly help people with problems, not cause more.
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Roger dodger.
Been waiting for those edits you were gonna do, but I know you’re probably busy. I decided to go the hardware flash route so won’t be needing them. I’ve just got one quick question (or two):
Is it possible to downgrade my current 5Mb Corporate SKU to a 1.5Mb Consumer SKU? And if so, how? I have a Series 8 ME.
Thanks!
@KraK0s - Yes, sorry, always buried here 
I can’t help without the files I requested from you
Or, wait till your programmer arrives, dump BIOS and upload for me, then do not erase or write anything until I reply back (in case dump is not good)
In your deleted posts, there is no checksum for ME, if you are seeing same image then you didn’t edit correct, or it’s OK/normal to see this error in MEA. Sometimes BIOS always like that, and it’s only visible if you extract ME FW and then look at it in MEA.
Since you are running into FW Update tool issues due to this size, you may not have cut it down to correct amount yet.
ME Downgrades are only possible within the ME FW rules (SVN/VCN) per that version you have currently, you can see these rules and how it’s all set here in guide + MEA for the info from each ME FW file. Sometimes you can go back with FW update too, sometimes not, and FPT would be required
Intel Management Engine: Drivers, Firmware & System Tools
As for what the actual issue is, I can’t say for sure, only guess based on your comments. I need to see both actual BIOS chip dumps, or whatever files you have etc (not modified by you), before I could give you any actual answers or provide any files to help.
Flash programmer is easy to use, once you have it and read a guide or two and then use it a time or three, don’t let it scare you 
AltMeDisable bit set is all you need done, I believe this is same as HAP bit = reserved = Yes. I’m no ME pro though, so I can’t say for sure, but I do know if your ME has the reserved setting I can disable it via that on byte change
I’m not sure on ME 5MB to 1.5MB downgrade, it may be possible, but there’s no reason for any of that, especially if your goal is to disable it.
Plutomaniac is the only one that would be able to say if this is possible, but I assume he’ll also agree with my comment above.