Are you on old or new bl?
which cwm5 and which cwm6?
When running IntSD-MountFix.cmd don't try to mount USB storage also. it must be unmounted.
Run again IntSD-MountFix.cmd and when you get the "Waiting for the device to enter recovery" connect the device (with USB storage unmounted).
I wanted from new BL to old BL so: old BL.
First I chose GB-twrp-2.5.0.0 from AIO v5.6. After the change from new BL to old BL and the fixing internal SD hanging in "Waiting for the device to enter recovery .." for quiet some time I looked on the latest posts here from people having problems with twrp and one guy mentioning you need an external SD if the internal SD fix fails. After writing with you I repeated Option 4 again with GB-cwm-5.0.2.8-ext. Again it was hanging on fixing internal SD. AFTER the hanging (waited 5 minutes) I tried to mount the usb storage in the recovery with no luck.
After that I chose Option 2 in AIO and there Option 2 for nvflash and tried to upgrade to GB-cwm-6.0.1.5. After the reboot and inserting the battery I still had cwm 5.0.2.8 installed.
After that I repeated once again the 4 Option with GB-cwm-6.0.1.5. Again it was hanging on fixing internal SD.
When I start IntSD-MountFix.cmd there is nothing mounted from me and i tried it couple of times now. Reboot to recovery, starting IntSD-MountFix.cmd, connecting USB device... leaving usb device connected, rebooted to recovery, restartet IntSD-MountFix.cmd
No luck.