If you are going to install a programmable ECU, you will have some more money in sensors, wiring, etc than just the ECU. It'll probably end up costing over $1k (unless you find a complete or mostly complete used system). If you don't want to spend a bit of time on this, your best bet is to find a stock ECU (assuming you now have the sensors you need to make it work). If necessary, you could buy a wiring harness kit from MS. It is definitely worth every penny.
If you do not have the sensors you need and you are planning to tinker with the boost, I would probably go the aftermarked route just for the flexibility of the system.