I've had this issue for a while now, if by the clunking sounds you mean that it sounds like it is trying to read the disc then makes a clattering eject kind of sound?
It's something to do with the loading mechanism for the disc, though I have taken it apart and can't find the problem.
However, what works for me and apparently some others is that if you lift the front of the PS3 and tilt it backwards 45 degrees or more just after putting the disc in, it then reads. Sometimes it takes a few attempts and occasionally you may have to do it again if it seems to be struggling to load something in the game. It seems to then work fine once the PS3 has been on a while and warmed up.
So try that first before swapping anything out. It's inconvenient I guess but I've learned to live with it, though I wonder if it might fail completely eventually (been like it for well over a year now)