I do the Edinburgh to Dunfermline Route a fair bit I used to use NCN 1 but have found the quiet country roads a lot better (the ncn is very narrow). You've not much choice other than to go by the bridge unless you want a 40mile detour instead of 2 miles. I do a route that takes me from Granton (North Edinburgh), to the north of airport (Burnshot Road), Standing Stane Road, Queen Elizabeth yard, through the south of South Queensferry and to the Bridge. I then rejoin NCN 1 (its on nice rural roads now) through Inverkeithing and up the back road to Dunfermline. I usually branch off then but the ncn carries on north, through the Cliesh Hills (great views up there too). You can branch to Alloa via the quiet B roads either north or south of the Cliesh Hill (South being more directish). Dunfermline, Townhill, Steelend, Saline. Clackmannan, Alloa.