!I’m having this dilemma at the moment. I have just fitted a new inner and ferrules/rubber shields. Shifting is fine, apart from the top 2/3 gears(big cogs), it feels very tight through the shifter. Is this a cable run problem or a set-up problem?”

could be either or both.
try relaxing the cable tension first. smallest on the cassette, release the pinch bolt and retighten the bolt without loads of pressure on the cable.

after that i would look at the last section of outer, a blast of gt85 might make a difference.

If you’re running full length outers how do you manage the cables under the bottom bracket?

The standard cable guides look like they will only accommodate inner cables. Is there a neat way of managing them?

If your cables run under the bottom bracket (road bike style) then to run full outers I don’t think you have many options other than to zip-tie to the frame – in which case you might as well route it normally (i.e. along the top tube and seat stays to the rear mech) so it’s easier to secure .

If your cables run under the bottom bracket (road bike style) then to run full outers I don’t think you have many options other than to zip-tie to the frame

Maybe no need? I’ve had both on MTBs that get ridden in year-round clag and find exposed outers under the BB / DT routed are a very close second to full outers. There’s almost no noticeable friction between a thin cable and that plastic BB guide and the outer ends face down so water isn’t running into the outer when it’s wet. A squirt of lube under the BB onto the guide is easy but generally not needed.