I would have to have a pretty trusting relationship with a shop thats going to align my boat. I suspect most wont do it properly, or at all. Its not difficult- just time consuming... so definitely a good thing to tackle on your own. Sounds like youre closing in on it.
Ironic timing on your decision to reuse the shaft. Yesterday my buddy broke a 5 year old ARE (which is a pretty high grade of stainless, no less) on a boat that was perfectly aligned. Dinged up his brand new $$$ Acme prop in the process. Shafts can and do break- so just be aware that youre reusing that shaft at a risk. His engine is a good bit healthier than stock, which surely contributed to the premature failure, but that shaft was perfect not that long ago.