The usual method is to melt out the potting compound in a slow oven,
catching it in a pan under the transformer (I hope you haven't thrown
the material out that you've already removed).  After the transformer
is repaired, just melt the potting compound again and re-pot the
transformer using the old potting compound.  That's the method I've
always used on antique radios.

The potting compound usually is tar-based and can be cleaned up with
a number of common organic hydrocarbon solvents.

Dave Vincent