Ok, to make a long story short I was able to boot in EFI mode after burning Fedora 29 live to a DVD and I ended up using a hybrid approch from what Hans said and the blog post, but...

I was able to tie in the Windows created EFI partition and just reinstalled the packages that install all the files instead of moving the files back over... Windows created a "Boot" folder under EFI and Fedora created a "BOOT" folder and I wasn't sure which one to use (or if it mattered).

I could run efbootmgr without issue or errors but the system still booted in BIOS mode. I even renamed /boot/grub2/grub.cfg and then it wouldn't boot at all, just dropped me at the grub command line.

From what I've read you're not supposed to run grub2-install on EFI systems but I suspect that my computer having an earlier implementation wasn't smart enough to figure it out, maybe running grub2-install would have fixed it since something was telling it to look for the BIOS_GRUB partition. 

I ended up giving up and just reinstalling Fedora and can report that everything now works fine. I had already completed a /home backup using BackupPC so after I got all the extra packages installed he was right back where he started.

On a side note, one problem I had is that grub2-mkconfig produced NO output when running under a chroot. I probably spent a good two hours on that alone which is partially why I gave up and decided to reinstall. After running "ps auf" while it was hung I figured out that it's the vgs call that was hanging. vgs couldn't talk to lvmeatd or whatever it's called. I never really found a direct solution but caught a reference about it not being able to find the runfile in /run so on a whim I added "mount --rbind /run /mnt/fedora/run" and voila, it worked! I've never needed to do that before...

Still didn't fix the problem since I couldn't get it to not look at /boot/grub2/grub.cfg...
 
And just to reiterate since I'm still seeing comments about it, the *ONLY* option in the BIOS on this computer related to EFI is whether to enable it for CD/DVD devices, which is why installing via USB resulted in a BIOS install. 

Hopefully if someone else runs into this they will find this thread useful.

Thanks,
Richard