I mean, it should work, there's no reason for it not to. However, in order for you to test what edits you've done to your save file, you'll have to use JKSM on the Homebrew'd console and test your saves on the console with the game installed.
You cannot mess up the CFW guide unless you are either A) an idiot or B) can't read basic instructions. I'm not saying that you are either of those, but the people who cannot successfully install CFW because of user error and something they've missed (like certain files, for example), not the guide itself. 3ds.guide is the only 3DS CFW installing guide that is constantly being updated to make installing CFW easier and safer. I have CFW'd all of my 3DSs and I've not had a failure, and I even followed the guide from when it was a Wiki page on Github and it was a lot harder and easier to mess up the install back then. You will be fine as long as you read the instructions carefully (and that includes reading over them a couple of times before you do the process) and make sure to take not of any warnings it gives.