Standard 2nd pitch we've always done goes out climbers left from the big tree up into the chimney/roof and then up to the same belay. Pretty sure that's the way Hill's guide writes is up.
Hill's guide does not indicate the chimney/roof combo for the second pitch of Second Coming - neither in words nor on the topo. Maybe you are thinking of Schein's guide "Sandia Rock"? Much better.
Anyway, I've never done the chimney variation so I didn't mark it on the photo.
An attempt at marking the route Second Coming. 1st pitch - mostly not shown; 2nd pitch - one variation shown and top belay can be rope-length dependent; 3rd pitch - rough approximation; 4th pitch - take your pick!