Samson pipes on v-rod

I recently installed the Samson Street sweepers made for the V-Rod. My V-Rod is a 2002 model. I changed to a high flow air filter and took the bike to harley to upgrade the ECM to the stage 1. The tech told me that the bike would still miss some due to the download is for the screaming eagle slip ons made by Harley. I test rode the bike after the ECM upgrade and it runs like ****! I called the tech and he said if I put baffles in it, it may help some. I then called Samson due to their installation instruction have in them if your going to install baffles, when to do it. Samson told me they have generic instructions and that they do not have any baffles for the street sweepers.
Do you have any suggestions on what to due to make it run better with the new pipes? The harley tech stated that I don't want to put a power commander on it, because it can fry the other computer components.
Thanks Hillbilly

Yes... The tech is correct but failed to mention you should install a Power Commander so you could actually tune the EFI correctly.

Odd that he would mention the problem but not a cure????

https://www.directparts.com/cgi-bin/dp.store/EN/Product/DS10200004

V-Rod Problems

Is there any thing else I can do?