When I did Wittig reactions, I used to generate the ylide before adding the electrophile.
If you plan to do the same and if you don't use excess base, the base you actually have in solution when you add your aldehyde is the ylide itself, a weaker base than the original BuLi.
And by all means, any other base you might chose would need to be at least as strong as H2C=PPh3, and you're back to square one...
As in many other cases, I think you must rely on chemoselectivity, i.e. you hope your ylide will behave more as a nucleophile than as a base. Aldehydes are very good electrophiles, you shouldn't have particular problems.
Btw, how did you protect the amino-acid moiety, if I may ask you?