Try giving Jordan a ring over at RK Tunes. I just used them for my Z4M Coupe and they did a nice job for a better price than anyone else (I paid $500 with O2/EGT delete and included shipping to/from for the bench flash). They are getting quite popular here in the NY/NJ area.
https://www.rktunes.com/collections/e46
If what you say about the ECU being the same as the e46, he should be able to help you out. Their site says $450 for 99-06 e46.