With remanufactured engines, everything rests on the reputation of the shop. Mack Boring has a good rep, and they also teach owners how to work on their own engines. Depending on where you are and timing...one opiotn might be to call someone there, tell 'em what you did, and ask if this could become a 'teach me how to work on my engine' in some way, so that you could be there either watching, or learning, or apprenticing in the rebuild. Can't hurt to ask.
Other than the rep of the shop, you want to know the warranty they'll give you, and that they are following full factory spec, i.e. not reusing anything that is supposed to be replaced during a rebuild. (Some bolts are torque-and-use-once, others can be reused.)
Even with reputation, if it is at all possible, eyeball the shop. A clean shop where no one is screaming, is always a good sign. If the floors and bathrooms are a mess--so's the work.
If you aren't comfortable with anyone local, I'd recommend Vosbury Marine in Annapolis. A family-owned business with a great name, absolutely top folks to deal with if they can take Yanmar. (I don[t give that kind of praise lightly.) They deliver on time, on price, and they'll tell you up front what your options are going to involve.