Underwater gear is available, just gotta get the right one for your boat. http://www.waterskis.com/200299-p/ma...ft_1_strut.htm
In terms of straightening I think you'd need to heat/anneal the strut, then ideally you'd know the appropriate alignment, and have a jig had some hardened points that you could use to align the strut.
As PureInboards mentioned, it has to be pretty straight - but I think the math misses one aspect - the engine is adjustable, therefore you can shift the engine to accommodate for misalignment of the strut.
In the alignment you center the shaft to account for droop, side/side up down for a neutral position.
Once you have that position you can shift/slide the engine, so obviously if the strut is out of spec, you end up with an engine that is not inline to the hull, BUT - recall that these are never perfectly inline, all engines are aligned to the strut. The stuffing box floats on a rubber tube to allow for misalignment of the shaft through the stuffing box/shaft log/strut.
Therefore my suggestion would be 1 - source shaft and prop. Heat and attempt to straigten strut. Install shaft, observe alignment through hull and at engine, if close - realign engine, bolt coupler and verify prop shaft turns freely.
If alignment is not feasible, then I would replace strut assembly.