I'm sorry I can not understand from your post what is happening with the projects that are screwed up despite the added info. DFH, Superior, and any playable instrument that is software we call "soft synths" which differentiates them from hardware synths which requires midi and audio(or just audio but...), if this were the case I can see the problem with things not playing correctly, anyway the soft synths are also call vsti as we of coarse use the vst protocol in windows and sonar, the i is for instrument to also differentiate them from regular vst fx like reverbs, compressors etc. no matter what hardware you change, or what order it's listed in, this certainly should not change the assignment of an "instrument track" or even the output of a midi track that is pointing to a soft synth, are you using instrument tracks?
when you're on a midi track or an instrument track and you select the input, at the bottom it has manage presets, have you been in there and made sure there were no midi devices checked that you are not using to play instruments? for me my mcu pro used to show up as inputs to some soft synths until I unchecked them in this location.
also have you tried to uninstal re-install the one you want at the top? mine are not alphabetized so this is still worth trying.
what i don't see you mention is if you have a dedicated midi controller or a keyboard with built in sounds that you are using, along with DFH, does the soft synths play correctly in the projects? I know you say the I/O's are all messed up, and you mostly want the FF400 assignments to play correctly, but what's not clear is your configuration that describes what the I/O has to do with the sounds that are already in the project.
Off Topic, I have a lot of old projects that does not play correctly due to plugins not being recognized because the plugin id is different even though they are installed and playable. I've upgraded many times and built brand new systems and I've have settled on not ever using on-board keyboard sounds, unless I turn them into audio tracks, things have gotten screwed up for me and I strongly advise a dedicated way of working that is as future proof as possible to avoid these types of problems.