It sounds like you might be getting ahead of yourself just a little. When you're learning a new song & chord progression, here's the procedure you can follow, even if you've been playing guitar for a long time:

Step 1: identify all the chords you'll need to know for the song. This means knowing the finger placement for each chord by heart. You should not be trying to remember where your fingers are supposed to go as you attempt to play the chord. Make sure you have the correct finger position first.

Step 2: Play the chord by slowly strumming or slowly picking each string so you can hear each individual note of the chord. Don't worry about rhythm at this point, just make sure that each note is the proper note for the chord, and that each note sounds cleanly as you play it. If you are hearing muted strings, identify which fingers are the problem, and correct it. If you can only correct part of the chord at a time, that's fine, for instance, just get the first 3 strings right, then add the forth, then fifth, then the sixth, making sure that the notes still sound cleanly.

Step 3: add a simple rhythm with each chord. Again, always make sure the notes are playing cleanly. If not, go back to step 2 and sort things out.

Step 4: chord changes. Ok, obviously you're going to change from one chord to another, but the trick here is to keep the rhythm really simple, play really slow, and work on making the chord changes in the order they will be in the song. Start with just going from the first chord to the 2nd, get that so its easy, then move on to the next and continue until you can smoothly make all the chord changes. Go as slow as you need to in order to make the changes without making mistakes. DON'T just play through "flubbed up" chord changes. If you can't make the change correctly with a slow paced rhythm, then just practice changing chords as slow as you need to without making mistakes. Going slow at the start will cause you to learn the song much faster than trying to go faster with lots of mistakes you'll need to correct later.

Step 5: Now that you know the chords, and can make the chord changes, you can start working in the correct rhythm of the song. Again, take it slow, and try to get it right as much as possible. Remember: you will learn the song faster if you go slow and make very few mistakes than if you try to play at full tempo but make a lot of mistakes.

Good Luck!