If they get knowledge of you detail stripping the gun, they may have issues with it.. In the past they have required a nominal fee to "reinstate" the warranty...also in the past they would still OEM parts even if aftermarket parts were added...example...if aftermarket sights, extended slide lock, single sided safety were added to a PT 1911 and you sent it in for a broken barrel link, they would fix the barrel link under warranty...if the safety malfunctioned...no dice. I might also add here that if you send a gun back in for warranty repair...if it's got tritium sights or special grips etc...good idea to take them off. If they decide to replace your gun with a new one, it comes back to you as an OEM gun with stock parts.
That's the way it was in history...it seems that policy changes like the wind these days...so be sure to ask and record the name/dates of your conversation.
edit....at this stage of your problem...I would probably try to have it ultrasound cleaned...your LGS or range may have the equipment if you don't. Might be the easy way to get crud out of places you can't see or reach.