If I were you, I would take out the cooler, the fans and radiator and start over again. I would also suggest opening up the other side panel and running the cables on that side whever possible to clean everything up and make it neat. Those rubber openings between inside are designed for just that and on the other side there should eithe rbe velro strap or places to loop zip ties around and bundle the cables together in a neat fashion. Cable management helps air flow.
Next just buy some thermal paste since you said you may have messed it up, clean off the old stuff from the heat sink and top of the cpu using a coffee filter/paper towel and rubbing alcohol and then apply between a rice to pea sized amount of paste, don't worry alittle too much wont harm anything.
Artic Silver, Artic MX4 and Noctua NT-H1 are all good thermal pastes.
When you get it back on I would suggest you mount the radiator to the front fans as I believe your case is more designed for that and plug the cable for the heatsink into the AIO_pump header and the whatever fans are blowing through the radiator into the CPU_fan headers.