If they have experience, that doesn't sound too bad at all. Really, if it was me I'd do it on my own or with some friends, but if you don't have the experience, time, or a place to do it, yeah, that sounds like an alright deal. Also, if they are in the habit of doing 2JZ swaps, it doesn't sound like they are the type of place that would say "Well, we need more money for this and this because we didn't know we would need that to complete it".
Remember though - 99% chance you will be getting a J-Spec 2JZ. Contrary to popular belief, J-Spec is not always better, and is especially true in the case of 2JZs. If you are content with stock or slightly elevated horsepower [or you plan on sinking more money in later to upgrade fuel, airflow and management], it will do you right, but remember that you will not be able to get max power with a standard 2JZ BPU[+++ etc..] kit, because the J-Spec turbos, cams and injectors won't flow or support it.