Yeah i felt the same way with my stock speakers after i upgraded to the pioneer that is in the car now.
After i found the alpine and the vega speakers another guy had a kenwood radio with 4 pioneer speakers for $75. I put the radio in the next day but it took me a few weeks before the weather was nice enough to work outside and replace the speakers. So i drove around a while with the stock speakers in it. I noticed a big improvement when i changed the radio out but when i changed the speakers out i was disapointed that there was really not much gain in bass or top end. The stock speakers really arnt that bad IMO.
The program i used is called "REW" its a "room equalizer program" for tunning speakers, the room, sound panels, subs. Its a free download if you search google. I used it for home theater speaker setup and placement but its a good tool for other audio stuff like this as well.
I installed it on a laptop, hooked the "headphone" out to a small amp, the microphone into the mic input and just ran the calibration and tested each speaker. I modified a small klipsch speaker box to fit the 6X8 speakers so i could clip the leads to each speaker after each test.
Its pretty easy to setup and use if you have different speakers to test.