If you can list your particular concerns about SR, I'd be happy to address them. The same goes for IR.
What vanilla spells do you rely on and in what way?
You might discover there's not as big of a problem as you think or I might learn about a problem and be able to fix it.Well, if you look at the linked topic, the last post is of Roxanne's ... I don't think she/he is satisfied with the given answers, yet. The background that Roxanne's mod comes from, is that of the BP + a lot of NPCs mods that were more of the core BP experience than anything else in the BWP installs. Aka of the non-SCS tree, to which you are heavily subject to...
I am pretty sure the short hand answer to Roxannes problem is to use spells with modders own prefix, and not the vanilla SPCLxxx.spl&SPINxxx.spl -files, with hoping that there is no dispel or protection spell needs etc that conflict. Yes, that can be a whole lot of mess if you are subject to it, in which case you are &%¤#!/(%&¤ . Of course there's also the healing spells ... so it's not a small deal.
I have already started that cumbersome task by using my own spells, items, scripts etc where I found issues. However not even that is a solution that always works, some tweaking mods (I cannot say if SR is among them as it is not for my use yet) run scripts that identify files they want to change by some fields (class, alignment, spell school, innate, or whatever.). Means the also tweak mod added stuff - and not only mine (just a large mod like Sandrah probably suffers a bit more than a smaller mod would just due to the amount of affected/infected files.).