I doubt you will have any luck with universal init.d since my app and universal use the same trick to get something done at boot time.
It really depends on your rom and accessories if thus method will work for you. My guess is that stockplus has removed the mechanism we used for boot time action.
Bottom line is that if you cannot mount the partition manually, these methods will fail. If you find out how to manually mount the second partition then tell me and I will add it to the app.
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I dunno, the OUYA hiccups for such random things it is really difficult to pin down errors. As of last night external storage was working. I need to run through all of my settings again though and double check init.d support in StockPlus. I'm using universal init.d at the moment, but want to check and see if the native support is working. With Bluetooth failing at one point during the night, who knows what bugs were popping up. I'm not faulting StockPlus, the stock code itself is full of glitches.
What I have is a 1TB Buffalo ministation split fairly equally in to ext4 and Fat32 (I tried to get Paragon NTFS working but gave up). I I'm using Android Tuner Pro and Folder Mount to do all of the work. I used terminal shell in AT and was able to mount the drive manually by typing "su" and then the mount command. . It was here I had all of the headaches getting the drive to mount at boot, then in the end used ES File Explorer to get the script in place . Once sorted out I looked at using Android Tuner vs. Link to SD to move apps on to ext4 partition. I finally decided on Android Tuner because of all of the other features I already use including backups and system tweaks. For the data folders Folder Mount is a cinch to use.
The only thing left to do now is sort out Nova launcher. For some reason when add shortcut for new apps is enabled, after boot new shortcuts for linked apps begin adding to home screen. The screens became a mess, so I cleared it all and will build new folders in the app drawer from scratch.