I feel your struggle. I'm in the same boat with the 00 ECU. I have the AIS removed and a custom PC map but it will not remove the hesitation and popping completely. I'm looking into having the ECU remapped as well.

I don't understand why you asked to sent the ECU back when they asked you for timing and fuel tables. Surely they could have provided you with (base) tables that would've more or less fit your setup?

It's not that easy to do it yourself I think. It can be done but how exactly is a mistery to me, the people that know keep it to themselves and profit from it.. fair enough it probably took some effort to figure out all the details. I think you can use Tunerpro software to make the connection between ECU and PC. I think its possible to make the physical connection to the ECU without opening it but no idea how the other option is to open it up like this guy did -> https://imgur.com/gallery/BwVNYko. That guy used some Freescale device with Codewarrior as you can see in this video -> https://www.youtube.com/watch?v=AREzSQXb9hU.

It's a bridge to far for me but if you find a way then please enlighten us