To set up the LCD controller when the clock is changed, follow this procedure:
One horizontal scan line consists of 320 pixels, plus a HSync period of 84 clocks (by default) - that is 404 clocks.
One vertical scan consists of 240 horizontal lines + 22 VSync lines - that is 262 lines or 105,848 clocks.
To get a display refresh rate of 60Hz, we need the clock to be 60*105848 = 6350880 Hz, or around 6.35MHz.
The display clock is set by the DISPCSETREG register. In that, you can choose a clock source and a prescaler. By default, this is set to 0x4A00, which means the source is FPLL, and the prescaler divides by 11, to the default display clock is 199065600/11 = 18.096873MHz. That's almost exactly 3 times what I'd expect it to be, so if anyone can explain this mystery factor of 3, I'd really appreciate it!
Anyway, if you change FPLL, set DISPCSETREG to (0x4000 + (((fFPLL / 18100000)-1)<<8). That should make the display adjust correctly. For example, for 200MHz, this gets 0x4A00, which is correct. For 100MHz, set it to 0x4400, and for 60MHz, set it 0x4200 (these won't get exactly 60Hz).
Play around with this, you may get some interesting results