So my acoustic guitar was pretty un playable the action was horrendously high. So i took off the bridge and filed it down, my own self mod and it worked out great im really proud. but now i probably want to put either thinner acoustic strings on it or maybe even electric strings. Will this affect the tone that much on my acoustic. Also if i switch to a lighter gauge string will the intonation get thrown off like it does with an electric?
i wouldn't put electric strings on. they are made for their conductivity, not their tonal properties.

the intonation might get a bit off, but you might as well try it for under $10 for strings. you just have to realize that you don't need to press as hard. that is the main cause of intonation messing up on light strings. people used to heavy strings press them and they go sharp.