2001 Dodge Grand Caravan 3.8L

Our van has 100,000 miles on it, has been seviced regularly and has just been diagnosed with needing an ECM/PCM replacement. Our question is this, while one shop quotes a new alternator and then the next shop says it's a map sensor and then the next shop wants to replace the modules. What's a person to do? We have a very reputable salvage yard that backs up all of their parts and has a fantastic service record, telling us that this is fairly easy to do on your own and that they will ship us one for $90.00total and our local dealership will "flash" it for $130.00total. The shop that has it now wants $1,000.00+tax to change the map sensor and to put in a remanned ECM, is this considered an average deal or are we being taking for a ride? Markup seems high, what would you suggest and is it easy enough for a somewhat skilled person to manage on their own?