I worry about using API's. I do not like the idea of giving my login info to a third party. I know it would be very unlikely that anything would happen but you never know. Sites get hacked all the time.
I have tried using the CSV imports with some of these tracking sites, however, as I mentioned before, some of my trades can have 50+ transactions each. Most of these sites provide a limit to the number of transactions before charging you. And the "unlimited" plan for these sites can be VERY pricey. This is why I am trying to find a way to do this manually.
If you mind spending more cash then I don't think any service can help you at all since generally they won't be offering their services for free without expecting any payment. The downloadable trade history via CSV files I think is enough for you to independently record all your trades from that point. I don't even think that you need to even go in that far in tweaking the file itself since all you need is all the trades you have made from that fiscal year.