Addition-only PHE in F#
You don't need fully homomorphic encryption for this.  In particular, you don't need to use Gentry's scheme.  Any standard scheme for additively homomorphic encryption will be fine.  For instance, Paillier should work fine, as should exponential El Gamal.

Search this site and you can find lots of information on additively homomorphic encryption.    See, e.g., Can Elgamal be made additively homomorphic and how could it be used for E-voting? and https://crypto.stackexchange.com/a/9003/351 and https://crypto.stackexchange.com/a/12704/351 and https://crypto.stackexchange.com/a/9139/351.  Also, search the literature for work on "encrypted counters" and you should find additional stuff that might be helpful.

This is not the site to ask how to implement crypto in F#; ask on StackOverflow for coding questions.  Your questions about padding make no sense to me.  The real question is what algorithm to use.  Once you know what algorithm to use, just implement it (that's just a  straightforward matter of programming).