MD5 has a collision probability of $1 / 2^{64}$ under the Birthday Paradox. Does this apply to any input given to MD5?
As explained in the other answer, $2^{64}$ is the birthday bound of messages until probable collision, not a collision probability. For two random messages you'd expect a $1/2^{128}$ probability of a collision with a 128-bit hash.
However, MD5 is broken with regard to collision resistance, so for two (or any number of) attacker controlled inputs you can't put a bound on it, they can find a colliding pair easily. (In fact, they can produce any number of messages that all collide, unless there are e.g. restrictions on message length.)
Also, is the output of MD5 uniformly distributed to the randomized input? (If, please provide references.)
This translates to "is MD5 PRF?", which as far as we know is the case. For a reference to the fact that we don't know how to distinguish it from PRF you can use e.g. RFC 6151, which uses that to justify why getting rid of HMAC-MD5 "may not be urgent".