Since you're not familiar with Linux, here's what I recommend: build the meta-doctor in Ubuntu, move it to Windows, and actually RUN the meta-doctor there in windows.
You don't actually need the SDK - you just need the Novacom driver. Even that, you only need to install it for the operating system you plan to run the Doctor from. Building a meta-doctor is unsupported under Windows, but you can run them just like you would any other Doctor once they're built.
I say grab the latest stable version of Ubuntu, install that within the latest stable version of Virtual Box, build the doctor as per the wiki instructions, then copy it over to host OS (ftp, CIFS, shared folders, thumb drive... take your pick), and then run it from there.
As far as the Palm Profile is concerned, you should be fine without doing anything to it. It certainly won't hurt to delete your backups and essentially start fresh, but you shouldn't have to Just like a non-techie upgrading his Verizon Pre Plus to a Verizon Pre2 doesn't have to do anything more than sign in.
For the PRL, that's not "once I get the meta-doctor..." that's something you should do right away to make sure you don't forget about it. It's a process that needs to start while running 1.4.5.
I don't know what you mean my ECR.
You don't need to worry about uninstalling any software or patches or anything - a Doctor wipes everything away (except /media/internal/, in some cases), so that gets done for you.
Only thing I'm not sure about is the hardware issue. I *think* you only need to swap the comm board, going CDMA-to-CDMA like that, but I'm not 100% sure. I'd like for someone else to chime in, since I'll be doing the same swap in a week or two.