Well, I think you got a great deal from the 2nd shop. I hope they can stay in business charging peanuts for a job like that.
Many shops tend to steer away from labour-intensive jobs like this because they can sell you a pre-built wheel with decent parts like 600-hubs and mid-range Sun/Araya/Matrix rims for $120-150/set. Takes less time (5-10 minutes to true & tension wheels), higher profits and the customer gets new equipment at a decent price.