I'm trying to get a cleaner sound from my guitar when strumming chords and am having problems when it comes to chords such as D because the bottom E and A strings have to be muted.

I have small(ish) hands and cannot wrap my thumb around the neck to mute these strings so I have been working on my strumming technique to miss out the two strings. However I find that I cannot strum the four strings cleanly as I am concentrating on missing the top two and as such end up hitting one string harder than the other three.

Any advice guys?
They don't necessarily have to be muted. Just play the 4 strings in D, rather than strumming all 6.
Make sure you practice strumming slowly at first.
Start with just playing D and strumming the 4 strings.
When you can do this flawlessly, play E (6 strings) followed by A (5 strings) followed by D (4 strings). This shouldn't be too hard because you are playing only 1 less string than before each chord change.
Then try some totally different changes: E-D-A, D-A-E, A-E-D.
pratice the right technic
try to it ONLY the 4 last string
with time and pratice , it will become natural and you don't gonna hit the E and the A string when playing a D chord

for sure it could take time , concentration , and pratice
but thats a huge part of guitar =)
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Nicely put good sir

I witnessed Night Of The Pear 2
practice makes perfect mate, keep at it.
ummmm, i dunno of it would work but maybe you could palm mute the top two stings, wait a sec, i'll just give it a go, well, i cant get that to work, maybe you could strum with your finger and mute with your right hand thumb, i got that to work
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just practise practise practise, and it'll just come to you, probably with out you noticing

do progressions like: G G G G, D D D D, C C C C, and that'll help you srtum different numbers of strings