I'm a bit unsure about the whole stacking issue.
Mods shouldn't stack IMO. You can apply 1 mod to a normal weapon so you often have the option to mod one of your current weapons (o/c there are exceptions e.g. magazine mods and rocket launchers). If you want to build yourself an Uber Weapon of Mass Pwnage (TM) you have to give up some inventory space to hoard those mods.
Phase Devices could stack for all I care. They are random enough and bring you closer to harm as much as they save you from it. I never ever bother with them so they might as well stack.
Meds are "guaranteed goodness", especially large ones, and stacking them would have a huge impact on balance. Also, I sorta like the offense vs defense choice that ammo vs medkit present ;)
Weapons and armors shouldn't stack obviously.
Either leave everything as it is or make the default ammo stack size bigger, reduce the inventory size and make the backpack increase it like you suggested.