The mod Redstone Control 2 is basicly ProjectRed but more advanced, it's microblock system helps create complex circuits.
Also, you an build a real control panel for the factory using the interactive microblocks.

Items to remove:

• power cable
• item cable
• fluid cable
• auto crafter
• block breaker
• item placer
  Removing these items makes the mod only do the logic part and not replace the function of create mod.

For balance reason, you could enable the circuit tester so that the players must build a logic gate with other mods and pass the test of the circuit tester to use the microblock version of that logic gate.
Btw, this mod requires CD4017 Lib
(It might be a good idea to change the crafting recipe for the logit parts to be like ProjectRed ones, you craft a single item and then use the stone cutter to turn it into other logic gates)