Is there a way of adding conditions on to custom formula where DJIA,SP-500 and Compqx are positive

or negative and will work on "any" time frame?

I do not know of a practical automated method of doing so as the Personal Criteria Formula Language does not have syntax for referencing other symbols. You may wish to review the following for a semi-automated technique for creating Relative Strength in a PCF:

Indexes in PCF's
RSMA PCFs

Is there a way of designing a custom formula for specific indices crossing above or below a ema?

You can just create a normal condition and use it on an index, but there isn't a way of referencing the index as part of a condition for another formula.