A stock of the show room floor TRX250R will make 32 to 34 HP on my dyno. A stock YZ 250, CR250R, etc off the show room floor will make 42 to 46 hp on my dyno. There is a big difference in the level of development that was put into the stock ports and exhaust on the ATC/TRX250R engine vs a stock 250 motocross engine.
If you do something to the ports on the TRX250R to substantially enhance the low end power with the stock exhaust you will decrease the power in the upper midrange and top end that is already low. Exhaust pipes that will enhance the low end will also hurt the power in the upper RPM range.
About the only thing that will give the engine more grunt is a very detuned big bore with a lot of compression and an exhaust system that is designed to grunt and not rev.
I have had a lot of customers that were told that their cylinders were ported for more low end but my dyno shows the opposite occurred. The problem is customers and engine builders have different definitions of "low end", "grunt", "mid range" "top end" etc. so it is very hard to define when there is a disagreement at what RPM low end occurs.
After many years of building engines and trying to match customers power expectations with dyno numbers, the majority of the customers are expecting a power increase in the 4500 to 6000 RPM range when they say they want more low end, mid range is in the 6000 to 7500 and top end 7500 and up.
In summary: I do not think you will attain the low end power of the 400EX with reeds, low end porting or any other modifications that will make her think she is riding a 400EX.