Thanks a lot for the help, the intonation problem is more or less over. However, the whammy problem still exists. My guitar does have a floating tremolo system, and I observe the problem the most while playing Eruption by Eddie Van Halen, after the first section.The guitar that I have is and Ibanez GIO GRG170DX, in case you want to check it out, I'm having a feeling it might contain some answer.
Thanks again
Ameen