Don't expect someone to give you an answer in 3 paragraphs in this forum when MySQL gives you pages and pages and pages of information and all you have to do is read it.
Finding the problem is a one-paragraph deal; open the application, see which operations are slow, look at the code for that operaton and see which queries are executed.
The general log only tells you which queries are executed and unless you are the only user at the time, you'll see a ton of queries that make no sense at all. The slow query log only tells you which queries take longer than some predefined limit. If you run 100 queries that take 90% of the limit each then you will never see any of them.
You are much better off reading things like the MySQL Performance blog, they have thought about how to find and fix performance errors and made it understandable.
They know how you read the performance schema and show which tables get too manu sequential scans etc (the usual culprit)