If I understand right you're talking about building your own headers/ extractors? A little leakage between the ports will have little or no effect. Don't worry about sealing 2 from 3. You're talking 0.5 to 1mm.

If you merge the pipes efficiently you can get good results with short primaries and long secondaries (much like the GX exhaust). This is because there's no overlap between 1&4, and , 2&3 so merging them is ok, only 1 cylinder is using the port at a time. The trick is minimising losses on the merge.