3 wk old acts as if something's in his throat

My 3 week old has thrush and his treatment is done in 2 days but he still has it. Every time it seems to be gone, a tiny bit comes back on the side of his tongue. I've been reading online that thrush can bother their throat so I wasn't sure if this is the prob or not but the past few days he keeps pushing his tongue out as if he's trying to get rid of something in his mouth but nothing's there and you can hear something in his throat when he's doing it as if he's trying to spit-up but can't. He coughs sometimes and his cry sounds hoarse so his throat must be bothering him. He's tired but it's making him fussy and he fights sleeping. Does anyone know what this could be or what I should do about it? I know it's not good but I've had him sleeping with us 'cause I'm so scared he's going to choke or stop breathing.