It sounds like most of your heat problems are realted to a poorly designed case.
Running it with the side off and a fan blowing into it is not a very good idea.
One insect flying into it could short something out and ruin the whole machine.
Water cooling isn't a very good solution either. It is complicated to set up right, unreasonably expensive, and any failure can ruin the whole computer.
Your best option is to pitch that case and get one that is designed for proper airflow.
Any case on Intel's Thermally Advantaged Chassis
list should give you acceptable temperatures using the stock CPU and video card heatsink/fan units.