dude, the stock heatsink isn't THAT bad - the chip only runs at like 1.3V, when I OC'd my e6400 i didn't even need to touch the voltage until i hit 3GHz. Temps don't start getting out of control until you start bumping the vcore up past 1.45V. I'd at least try to hit 2.6GHz at stock voltage. that will give you a better comparison on the performance improvement of a C2D over an A64.
And yes, the RAM is part of your problem, for 2 reasons - a) it is running in single channel and b) the bus on the e4300 is really slow - it's really only fast enough to support DDR2-400 at a 1:1 ratio - your bus is only running at 60% of the speed of your RAM. C2Ds are much more memory bandwidth-hungry than A64s, which really only cared about low memory latency. Adding another stick of memory and/or OCing your FSB to take advantage of the faster memory will help out quite a bit. if neither is an option, try slowing down your memory and seeing if you can reduce your memory timings - running your RAM in 1:1 with low timings will produce better results than running your memory faster than the bus with high timings.