Unfortunately, there are some hidden sections which are not indicated by the SoulStorm bottles.
I recommend going through the Abe's Exoddus FAQ on the
www.gamefaqs.com website.
It keeps a running tally of all the mudokons you should have saved.
Try and save once for every region you have been through, and make sure you keep an eye out for secret areas. Most of them are quite easy to find in AE, compared to AO.
The most you'll probably miss are in Necrum Mines. There are a couple found by going down to the next level (although it appears to be a death pit), or rolling through a hidden area.
Make sure you get every mudokon in the area to work on any of those circular valves before sending them through the bird portals as well. Especially in the Blind Mudokon area of Necrum Mines.