Finally something I know about.
Firstly, it weill benefit from a good application of silicon on the joints. Thats the job for when you have some spare time. Then open and close it with the engine runing.
There is a release on the UK car so assuming the JDM is the same, look in the cubby behind the passenger seat, the big one. With the passenger seat right forward you should be able to see a plastic cover in the top of the cubby. In there is a toggle, pul it and this should release the mechanism and allow you to open or close it fully.
Once it has been put in open or closed the roof should reset and allow normal operation.
Let me know how it goes.