I think you'll be disappointing with how hard it is to seal on the bottles. THey flex so easy and it is just going to be a mess. Sealing under pressure is even harder.
Also, if you put the pump at the bottom, it likely means you could drain the whole tank when the seals fail.
If you really want to diy a filter, it'll cost more, but I was happy using whole house water filter housings, pvc pipe and an inline pump. A submersible pump could be used as well.