I think with a customized 5.6 that the results would be unpredictable at best. I have many contribs & other things running in ibays but will reluctantly zap them all & recreate on my brand-spanking-new 6.X server ... once I get the hardware & Lycoris provides the software, that is!
In short, you could try it but I don't think I'd trust the resulting system. You could always clone the hard drive and try the upgrade on the clone, then work to fix what broke & re-clone if necessary.