I've never been to CGK but can share my thoughts for SIN and KUL.
2 days in SIN might be a bit too short. It depends on what you'd like to do? Are you in interested in shopping? Sentosa can take a whole day. Then there's the zoo and the night safari, lots of shopping malls, Clarke Quay...
I'd say 3-4 days would be ideal.
Maybe arrive in SIN early morning and depart at night. You'd then have about 4 days

KUL: It was an OK trip. Much prefer SIN. I stayed 2 days and it was enough for me.

There's a sleeper train from SIN to KUL.