Using a mana surge rune while a mana surge rune is active results in the second value being multiplied by the first. With a bit of finagling I managed to get my mana regen up into the 300k range pretty easily (I won't go into how exactly But it's legit).
Maybe mana surge runes should be disabled while mana surge is active.
Yeah, the way it stacks multiplicatively is part of the problem. Leads to the mana restoring spell being overpowered too - so powerful there's no need for more than 1 point in it.
Well another way to go about it would be for mana surge to just give you X mana regen per turn instead of multiplying current mana regen by X.
Mana Flow was part of how I got the numbers so high but keep in mind that the current system also prevents mana surge at all if your mana regen is below 0. So if you're sustaining Thunderstorm for instance (which is why I started experimenting with regen) you can't use mana surge at all.
Dividing the multiplier by 50 and turning it into an addition to current mana regen would probably work well (the starting rune would regen for 12 per turn, high end runes would give 30 per turn) and allow it to stack nicely with Mana Flow without being overpowered. Again though they wouldn't stack with themselves (which they probably shouldn't anyway, 99% of effects in the game overlap rather then stack.)
Granted, I think DG's original intent was for mana surge runes to be better for natural casters and worse for shadow and arcane blades (unless they figured out some non-native means of mana regen) and my suggestion doesn't facilitate that.