First, to illustrate Felix's point about the consequences of using a soft link. Considered from just a safety point-of-view, I personally would only use a riveted link on a 998 chain. If you don't have the proper tools to install (one or more) riveted links, have your dealer do it.
To address your questions:
A 525 and a 520 chain (having the same number of links) have the same length, i.e. the same distance between links, but because they have different widths, they need different width sprockets.
If your rear tyre is contacting the larger downpipes you need to add two more links (total 98) to the chain to allow the eccentric to move the axle toward the rear of the bike away from the pipes. Chains always have an even number of links (alternating inner-outer plates.) Remember to record your ride height at the 4:30 position first.