Emperator: The standard setup of the shock position, kickup, caster, rear toe-in, etc as in the manual should be ok as it is been tested already. you can change afterward depends on yer track condition and size.
tire choices is alot. also depend on the track. im using Sorex 36R with speedmind medium insert(red). im running on a hot day so, 36R is the best grip. But of course yours is different with colder weather.
Ask around especially racers at yer track. if can, get friendly with the best racer at yer place. he should know what tire to choose and setup for that particular track u run.