A method call has the same base effects of a regular function call. Values are pushed onto the stack, and new code is executed. With methods, the only difference is an extra call to get the object for which the method is being called.

It sounds like you have a bad case of spaghetti code. A first step would be figuring out the "when" and "why" the functions are called. Understand the problem insie and out. Finally refactor. Identify the loops that the function call loops it goes through and find a way to break it.

Wish I could help s'more.