Extracting Randomness from Mouse Acceleration
Start by reading How to extract randomness from a file?.

At a broad level, it seems like you understand pretty well the techniques.

To extract randomness in practice, I recommend you use a cryptographic hash, and use techniques from the cryptographic literature for cryptographic building pseudorandom generators. 

You mention "extractors".  I know there's some cool theory surrounding them, but I don't recommend you use extractors.  They are beautiful but not practical.  Cryptographic hash functions are superior in practice.

You talked about estimating the amount of entropy in the data.  Unfortunately entropy estimation is an inexact science.  It's also easy to over-estimate the amount of entropy (e.g., if there are non-trivial correlations in the data that you didn't think to check for).  So, a typical procedure that cryptographers often use is to make some estimate of the entropy rate (typically through a priori calculations), then divide by a factor of 4 or so to provide a safety margin -- and gather random values from many sources, and feed them all into the pool.  The hope is that even if one source provides low-entropy data, or even if one of the entropy estimates is too optimistic, maybe some other source will have enough entropy in it to make up for the problem.

Overall, I recommend you spend some quality time in the cryptographic literature reading about the techniques that have been developed there.  Cryptographers have spent a lot of time worrying and thinking about this, because cryptography relies upon high-quality random numbers.  And, rather than re-inventing the wheel yourself, it's probably better to re-use some existing well-tested cryptographic method.

Here are a few pointers to get you started:


https://crypto.stackexchange.com/q/41967/351
https://crypto.stackexchange.com/q/27028/351
https://crypto.stackexchange.com/q/32984/351
https://crypto.stackexchange.com/q/10517/351
https://crypto.stackexchange.com/q/18355/351
https://crypto.stackexchange.com/q/39186/351


You can look around Crypto.SE and the resources mentioned there, and you'll probably be able to pick up a bunch about this topic.  Have fun!