Did you impregnate the old headliner material or did you use another type of fabric/ FG Cloth? After allowing the resin to harden did you use body filler to cover the surface? Did you fully impregnate the material you used?
If you used enough hardener and fully impregnated your material you should not have had these problems. With some use of body filler and paint you shouldn't have a big problem fixing it.
It looks good in most places that I can see from the pictures.
Good luck.