part 1:
no, there's no difference in sound between RCA and 1/8" *
1/8" is usually stereo... RCA is usually (always?) mono
so if you wanna process each side of your gameboy tracks individually, RCA is cool because you have a separate output for each side built into your gameboy.
most mixers and stuff use some combination of 1/4", XLR and RCA... hard to find gear that will have 1/4" inputs... but you will probably be buying adapters whatever. 1/4" and XLR are both usually/always mono so RCA might better from that point of view... direct 1->1->1 relationship from gameboy->adapter->input
i would go with RCA but if you have stuff with 1/8" input (pc motherboards and laptops usually do, can't think of much else) and you aren't planning to get more gear then i guess go for that
one advantage of 1/8" is that you can plug headphones in but if you leave the original jack intact when you prosound you can do that anyway
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well, there is a LITTLE bit, because one is two cables and one is one cable. you're unlikely to hear this in effect
part 2:
i'm not sure it's possible to switch the CPU in a gameboy very easily at all... it would be easier to just buy a different gameboy. but i think all the DMGs are the same speed really. if you want it faster you should get a GBC or one of the advance models (not the micro!).