Is there any way to make Heal work on Mechanical units instead of organic?
Probably not...
How about making Repair an autocast ability?

Did you try checking both organic and mechanical flags?

For heal?
I can't find the entry in weapons.dat
So I'm assuming there isn't one?

No, as in going into the entries for the units you want to be healable and checking their "Organic" flags. Keep in mind that this will also make them valid targets for Irradiate.