What are the hardest topics to understand in AP Biology?

When I have taught with this text, the biochemistry section seems to be where students struggle the most.  This includes the cellular respiration you mentioned and photosynthesis.  Cell communication also seems somewhat tough so chapters 9-11 in Campbell 8.  

The next most difficult seems to be genetics (14 and 15) not because the material is as detailed as the biochemistry but because the way to learn genetics is to do lots of practice problems.  Just reading the chapter won't be enough, you need to practice the process.  This also holds true for population genetics in chapter 23 (Hardy-Weinberg problems).

Cell respiration is a tought one, if you plan on taking biology/biochem in college you will probably have to learn it agian...and then again in graduate school if you go that far.  
However if you need some help. Go to www.pubmed.org and select books. You can type in a topic and access a number of different text books. Sometimes a different view point helps

The hardest part for me was Genetics. Cellular respiration was sort of tough, but enough repetition and deconstruction of the words into their roots and affixes helped me.

Seriously, I HATED genetics. I could understand the mutations and such, but something about dihybrid crosses never stuck in my mind.

Cellular respiration was a mental image in my head for my tests: glycolysis, Krebs cycle, and phos. oxidation... Just re-re-re-re-read everything and draw pictures (with the mitochondrion in all pics, because that will certainly be a question: "Where does ________ take place?")