The 3GS has the ARMv7 processor clocked at 600Mhz and the iPT4 has the A4 clocked at 800Mhz, so there should be a difference...it may be the difference in screen size that cancels it out, though.
It's not 1 GHz. They both use the same Cortex-A8, SGX535 GPU, and 256MB RAM. The difference is that the iPt4 has the CPU clocked at 800 MHz instead of 600 MHz. But due to the large bump in screen resolution, differences in speed are usually minimal.
When you said: But then I googled it and saw that the A4 has the Cortex-A8 in it... Sorry if I sounded like a douche