I'd go with 4.0, the AMCAS way. Though schools would probably figure out that you didn't take 1.0 credits of organic chemistry, I think it's just easier to bypass that and use the normal credit system. Esp. since lots of schools say clearly 8.0 semester hours of physics/genchem/bio/organic, it's easier to just do it that way since it's on your AMCAS anyway.
I've never heard of that system, it's weird! Out of curiosity, are all classes 1.0 credit no matter how often they meet? Like, my school has 1.0, 2.0, 3.0 credit and 4.0 credit courses based on how many classes per week it meets (and I think a couple 5.0's). Do seminar classes that are 1x/wk count the same in your GPA as a 3-lecture+1-lab class? What a headache for you!