You can power that controller chip (I suspect it's going to be a TL494) with 12V and check you have a clean switching waveform to the transformer and then on the other 'hot' side of it.
It is a TL494, nice guess. I put 12.5V into the Vcc and the chip output 4.94V for its 5V reference. C1 and C2 of the chip oscillated at 113kHz with a 61% duty cycle, 0.5VAC. Interestingly, the frequency setting capacitor oscillated slightly on the CT pin - 103kHz 43% 0.002VAC.
It seems to be a pretty standard sort of configuration to have a transformer driving the power switching devices when the control chip is a TL494, I've seen it in various places all the way back to power supplies in power supplies for clone 286 PCs and it just looks 'familiar'..
You can find dozens of PC power supply schematics all over the web which are all using the TL494 in extremely similar configurations (I'd bet the circuit is almost identical around the TL494, it'll just have a few differences on the hot side to accomodate the MOSFETs):
http://320volt.com/wp-content/uploads/2010/12/atx-smps-schema-200x-atx-power-supply-tl494-lm393.pnghttp://www.eleccircuit.com/wp-content/uploads/2008/08/200w-pc-power-supply-110v-220v-by-tl494.jpghttp://www.eleccircuit.com/wp-content/uploads/2008/07/old-power-supply-computer-by-tl494.jpghttp://danyk.cz/s_atx01g.pngThe chips are dirt cheap so you can check it by substitution
Usually drives a couple of transistors from C1,C2 output which in turn drive the transformer to get the switching signal to the power MOSFETs.
Check the drive is clean all the way to the transformer, that both drive signals are the same at the transformer and that you get a clean switching signal out of the other side of the transformer.
On the hot side of that driver transformer there should be a small circuit that 'rectifies' the drive signal to make sure it doesn't go negative and a little filtering. Check those diodes.
As it's using MOSFETs for the main power switching there will probably also be a Zener clamping the gate drive to something like 15V, check they're good as well.
You should be able to follow the PWM drive all the way from the TL494 to the gate of the power MOSFETs with only the 12V supply to the TL494, same again, check the drive signal all the way from the transformer to the power MOSFET gates.
Once you've got that clean, I would remove your mods and get the supply working as it was designed first, draw out the schematic if you haven't found one yet, then try to mod it on paper before you add any solder.