Yeah, three pounds carried up and down a gazillion miles' gross elevation can and will make a difference. It will affect your daily range and perhaps the overall health of your legs.

I also think you can consider not relying on a single shelter for the duration--once you're in mid-season you might be able to downsize to a simple tarp then, depending on when you hit Washington, moving back to the more rugged shelter.

I've never completed a multi-month trip but I think of them as a collection of shorter trips and with the PCT, across a hundred different settings. Your "drift box" should be stocked to allow changes on the go as conditions and your conditioning change. Not to mention, you can celebrate the end of canister territory by sending the thing home.

Happy planning!