The failed rectifier may have affected the stator windings. Also older SV are well known for corroded connectors, and a good clean plus ACF50 spray seems to be the mutts bits for that, and maybe while you are on wrap some self-amalgamating tape around them to seal out further water entering.
https://www.toolstation.com/self-ama...ir-tape/p23876
Search on forum for 'charging' and 'lumpy running' or other key words or phrases that may cover your problem, there is a massive amount of information already on here. I must admit that sometimes it is easier to search from outside the forum in Google, Bing or similar - just spell out the problem and add SV650 or SV650.org and this site often comes up bang on the thread you want..
This search in Google
battery charging problems sv650.org is how i found this.. ( and a lot more threads on this forum)
https://forums.sv650.org/showthread.php?t=109555