I'm not an expert on this, but it looks to me like there was water leaking into the 3rd cylinder, which has damaged the piston. To answer the question you posed, yes, I think it will create a problem. It looks from the picture like the top of the piston is pitted, which could be corrosion or detonation damage. It will eventually fail.
The other possible downside is that if you get the head all nice and tight, the bottom end may not be able to handle the extra compression (because it no longer leaks), and you could blow out the bottom end.
It would probably be much cheaper to rebuild that motor than do a swap, but if your ultimate goal is to go EFI, then I would probably start saving my pennies, and move that direction. With some tweaking, the 20r motor can be a great little powerplant. You could just get the head done, run it till it dies while your saving $$.
Just my $0.02
Erik
