Yikes!!! This is a mono cast frame, there is no reason the frame should not align to the engine. Maybe you bent the engine block?!?!? :don'tknow: :shakehead:

<< j/k, just don't wanna see your frame fracture.
I suspect, that both the engine gaurd likely pushed the engine forward slightly causing the offset. I doubt it, but if the bolt as loose AND there was enough forward pressure from the gaurd,
possibly, it sheared the stock bolt apart... The engine being offset by approx 2mm is alot and the question is, WHY????
If you removed the gaurd and loosened the engine, everything likely would have lined up (maybe with a slight bit of support under the engine too as your working against gravity). Guess its a moot point now.
8-10mm thread depth, (maybe 7/16")
is very little (I guess better than nothing) but I seriously doubt it'll hold 40 foot lbs(maybe grabbing the rest of the steel bolt still lodged in the block)..
IMHO, as a member previously posted, if it was my bike, I'd loosen the engine and let the front of the engine drop just enough to clear the frame (after removing the gaurds).
Then get whatevers in that hole out, and heli-coil. It'll be stronger that the original hole if centered. BTW, that hole, now offset slightly forward, will weaken that aluminum mount on the engine. Should that break, you now have some much more major issues to deal with..
I'd also modify that gaurd to fit correctly, open the hole, re-weld, something...
Good luck