I am not a flake expert so maybe wait to have the usual nix guru here, but here is my understanding. First flake does not really like inputs (see that ongoing discussion). However in your specific case I guess you don’t need inputs and can use instead _module.args (there is also specialArgs but it is not really recommended as discussed here). The idea is to change your modules to accept an additional input (e.g. in your case the set of inputs listing all your flake packages):
{ config, pkgs, remoteConfig, ... }:
Then, you can use remoteConfig in your configuration, to call packages, modules… And you provide this value in your configuration:
modules = [
{_module.args = inputs;}
./configuration.nix
# …
An example of PR doing that is given here.