As I see it, to do Salford Crescent - Broad Green - West Kirby you just need your original ticket. That is a perfectly valid route and no excess is required. Take the excess coupon you already have off, and if there are two staple holes, so what? That doesn't invalidate the ticket.
Salford Crescent - Atherton - Wigan Wallgate (code is WGW btw) - Kirkby - Liverpool Central - West Kirby is a permitted route on a Salford Crescent - West Kirby ticket, as that is no more than 3 miles longer than the shortest route, so no excess is required. It is not permitted via Bolton as that would cross the 3-mile threshold, and there is no mapped route via Bolton so you will need two tickets. No excess can be issued. That said, online journey planners use a different set of distance figures and the threshold is more generous, so if you can get an itinerary from journey planners via Bolton then you can legitimately travel that way. In reality I doubt you would encounter problems either way.
To do Salford Crescent - Earlestown / Warrington Central - Liverpool - Kirkby - Liverpool - West Kirby, the excess you were issued with is not valid, because the excess changes your ticket from a Salford Crescent - West Kirby one into a Salford Crescent - Kirkby one, and the validity of your ticket ceases at Kirkby. You would therefore be required to purchase another single ticket should you wish to continue from Kirkby later. If you only wish to go as far as Kirkby then provided that this excess is issued, you can legitimately travel there. That said, I can't see any reason why this excess should be issued in the first place, as it fits none of the legitimate reasons under which an excess can be issued. The correct course of action is for you to purchase an additional ticket for Liverpool Stns to Kirkby as this is deviation from your permitted route.