As Eric said, 1100, 1300 and 1500 CARB manifold gaskets are the same, the FI gasket has the notches for injector cutouts.
I wouldn't cut the notches in the carb manifold, all you will do is increase the cross sectional area locally and slow the inlet velocity, as well as shifting the centreline, and creating port turbulance... the mix and match of FI and carb parts isn't ideal as I've said before, but if those are the parts you have to work with then they will have to do.
I also wouldn't port the head / manifold to suit the gaskets, or once again you will have a localized widening of the cross sectional area at the gasket face (gasket is about 30mm dia) and the whole idea is to have an even and gradual taper down to the port throat which in your case is around 28.5mm.
Filling the injector notches would be a better solution, but I'm not sure if I would trust devcon - jb weld type of fillers to stay put and not fall out and run thru the motor.
SteveC