I think the best way to go now is not to try desperately to adept the loader to work perfectly with Wiigator's DIP module, but instead start building a new one altogether. The reason is that however good the loader can be, it still relies heavily on a proprietary DIP module which is, to be completely honest, NOT perfect. So when this project has it's own (open-source) DIP module, it'll be a complete package to play backup games and it'll be able to rely on the (coding) community to perfect it's performance.
So, instead of trying to indirectly fix the things in the (proprietary) DIP module that are already inherently broken, you/we should start from scratch and don't let those problems slip in in the first place.
Of course, if there is a possibility of not using a cIOS at all, but for instance patch the DIP module into any IOS, that'll have my vote. Mainly, because games can then be run on the IOS of their choice, improving compatibility greatly.
P.S. WiiGator, really no offense to your coding, I think everyone here can agree you did a tremendous job on your loader and especially the lightning-fast DIP module.