First thing, replace the thermo if you haven't recently. It's possible it's sticking and not openning fully or even just seized halfway so it still allows flow but not fully. Regardless, they're not expensive and not really hard to get to, so it's good idea anyway.

Next issue you may have is the fact that your running a larger, more performance oriented engine with a stock Civic half sized radiator. Depending on how old your car/radiator is, that can also play a factor and if you don't have A/C or removed it, you need to block off that opening or most of the air will just skip right past your radiator.

In my opinion, you have 2 options. Go for bandaid solutions or upgrade your cooling system. I use the term bandaid but it's not as bad as it sounds. Running a higher precentage of water than a 50/50 mix for coolant and adding something like water wetter will help keep the cooling system from boiling under heavy load. If you live somehwere it gets cold in the winter, your going to have to drain the system and refill for a 50/50 to keep it from freezing and damanging the block. A lower tempurature thermostat and higher pressure radiator cap will also help. If you want to just fix the problem and not worry about, a radiator upgrade is the best solution (besides, it's a Honda, we have these options). I used to risk overheating my '92 CX/B18C1 hybrid with a lot of high speed (85-90 mph, just keeping up with traffic) highway driving on really hot days (that's better than 4000 rpm with a GS-R tranny). I upgraded my car with a fluidyne radiator and never had another problem. Just something to consider.