2015 Scrambler Sputtering, Any Ideas?

Hi all, I have a 2015 Scrambler, I had a Zard exhaust on it but had to switch it back to the original so that I could pass the safety control inspection we have to do here in Spain every couple years (The Zard is way too loud). So I put the stock exhaust back on myself and took it to a dealer to remap it for the new exhaust and since then it sputters and jolts a bit. Mostly noticeable when on lower to moderate throttle. (idles fine)

Couple clues...I have some suspicious my battery might be nearing the end of its life, but could that cause this?

Im also wondering if the cause could be that when I put the stock pipes back on I didnt do it properly and there is a small air leak where the pipes enter the head?

Or I guess it could be any other number of problems. But I failed the safety control because the sputtering/mini backfires surpassed the noise level permitted by law.

Any ideas?

 

Yes, I bought this EFI bike partly because of all the "fun" I thad tinkering with the carb on my 79' Enfield. Happy to now be rejetting. Although also not so happy to be re-mapping. Didn't know the fact that it can take some time for the remap to adapt, good to know. But I don't think that's it. I've ridden it a good 150km since.

I think it's an air leak. When I put on the Zard I reused the copper gaskets, And once again the same gaskets when I put the stock pipes back on. I think Ill try and refit them with new gaskets.