Unfortunately there is no such thing as a cheap, well built hot rod especially if you have to farm out major work. I have done numerous major swaps over the years (believe me anything that requires engine/tranny mounts, exhaust, cooling etc to be fabricated is major).

Chances are you friend is actually being under-charged. From personal experience in my own shop and working in others you seldom charge for all the hours you actually end up having in the project. A good example is the motor mounts, I'll charge for actually fabricating the frame mounts and the materials involved and also a little for the time lifting the engine in and out and mocking up the templates and welding the mounts in. What is not counted is the time I spend looking though parts books for the motor mounts that will work the best and provide the cleanest installation. Also not charges is the time spent just looking at the mounting points and determining what the finished mount should look like. Then there's always the little things like the trip to the parts house for the longer/shorter bolts your going to need that you just don't happen to have on the shelf.

As a transmission swap is also involved, you are also looking at fabricating/modifying clutch and shift linkage. While the actual work may not require a lot of time, several hours (that are not normally charged) may be spent figuring out what exactly needs to be done/built. You also mentioned a disc brake conversion. From personal experience your friend will be charged for the time to remove the old components and install the new ones, but if the shop has never dealt with the particular kit they are using, there will be the time spent going over the instructions (some of which can really suck) and figuring out exactly how the kit goes together plus scrounging the little parts that are not included which is time not normally charged.

I would get involved in these projects because I enjoyed the challenge of figuring things out and making them work. The down side was that I could have made more money doing strictly service work ( which is a big reason most shops would not even consider doing this type of project).