LTTE was in a position in strength throughout 90s and early 2000s, but his arrogance ultimately led to his downfall. Also you are forgetting how he alienated Col. karuna who was effectively #02 in the organization.
I am telling same thing if you don't the details stay calm. Prabakaran ran parallel govt. and he followed tamil culture according to their law , rape is punishable offence( death sentence). Everybody is same infront of justice ryt Karuna raped a girl and proved with evidence so their court issued death sentence to him. To save his life he got asylum in SL govt. .Karuna is not no.2 he is one among the top commanders.