I just did an N64 RGB mod, and of course got the crosshatching. I am considering doing the C-sync mod where I cut the trace to pin 9 and run a wire from 3 to 9. I am wondering, will this affect the systems Composite or S-Video output in any negative way?
You will have no composite video if you do that. You could run them both to a switch to have both on pin 9.
here is another option. a cable that gets sync from pin 3: http://www.ebay.com/itm/Super-Ninte...W-SYNC-cable-cord-US-model-SNES-/161167675711
Use pin 3. It's composite sync, that's fine. What components you put in the SCART cable depend on what mod you did, and the levels you're getting. If you need to strip sync from a composite video source (Famicon maybe?), you'd use a sync stripper, but you shouldn't need to for this. http://www.mmmonkey.co.uk/composite-sync-stripper-lm1881/