It could be a multitued of things here what you will have to do is explain its movements with more detail

When you say all over the place do you mean forward / backwards or is it spinning on its own axis etc

Blade clacking ( when the upper and lower hit ) accurs when there is too much input to correct. The easiest way to fix this problem is to get an extended inner shaft to increase the distance between the upper and lower rotors, but flying indoors this should not be required as your stick input should never need to get them that far. I take it that its not spinning on its axis (yawing) because you mentioned the blade clacking.

As far as tracking the upper rotors ( you cant with lower).

On top of the upper head there is a small link linking the metal flybar to the ball link on the upper blades, to adjust tracking simply pull off one of the lugs and you can twist the lug on the screwed shaft to lebgthen or shorten the link. Run the notors up so that the blades are fast enough to see if the tracking out, then power down and lengthen the link, if the trackings better but not perfect the next time round then do it again, 1/2 a turn at at time. If the trackings worse then twist the other way shortening the link until trackings very close

You wont ever get tracking perfect but very close will do.

The tracking of the blades will not have any efect on blade clacking as only very minute adjustments are needed.

It could be loads of things, gear slipping, swash seperated, rotor heads loose.

Explain its actions in more detail and we will find the exact problem in minutes