I have a Titanium frame that needs aligning, the wheel is not centered between the chainstays. I dont think it was always like this and I suspect it might have happened when I had a big crash a couple of years ago.
It must have been out of alignment for a long time before I noticed so it might be you can just build up your frame as is and it will be fine. Since building my own frame I tend to notice frame alignment and there are several riders in my club whose rear wheel is way off and I dont think any of them realise or notice! - expensive bikes too!
I do have some experience of bending grade 5 titanium (not with bike frames or tubes however) Heating to a dull red makes it much easier and will not affect the integrity of the material like it might steel, this is probably not necessary for the small bends we are talking about, but might be worth trying if you fail to manage it cold.
If you do try and bend your frame I would suggest having it clamped rigidly at the bottom bracket and have some method to control how far you are bending. Increase the bend distance a little at a time until the stay springs back to the desired position (measure between drop outs) Then do the other stay. Adding this level of control should prevent over bending.
One thing that has been puzzling me a bit and maybe the experienced builders here might be able to explain: If you have bent the rear triangle slightly and the wheel is now closer to the left hand chainstay, which way do you need to bend the stays to re-centre the wheel? Moving the drop outs to the right seems the obvious way at first but since they will be moving in an arc, the RH chainstay will be getting shorter and the LH longer which will rotate the wheel rim towards the LH chainstay making matters worse.