A clarification...most of the time, if wording mentions staying within design parameters, it means it can be compensated for by the rest of the system, NOT that it won't affect it.
Kind of like the 3" SL for the pre-'05's...sure, it messed up the alignment, but not beyond the available range of adjustment to get it aligned again.
Most of the time, especially for a modest SL, you can just loosen the brake line attachment points, and flex it out to see where it goes...and then relocate/re-attach as appropriate.
Chances are the front IFS travel won't change a whole lot, you are just pre-drooping the suspension to get lift, eating downtravel to get more uptravel and ride height....so front shock travel will probably be fine stock as far as length goes.
I haven't measured a rear shock on a '05, but the pre-'05's shocks were too short to take advantage of the 3" SL.
The longer shocks really let the rear droop much further.
I'm not sure if Darlington Skidderz fit the leaf packs on the '05's either, but, if they do, going with the top mount shock version would let the stock shock, or a longer one too, droop further before running out of shaft.
Check the lengths of the breather tubes too, not just brake lines...I forgot to do that on a lift, once,...not pretty when the water gets in there.

_________________________
- TJ
2001 Xterra '03 VG33, SE 5 spd, 305/70/16's, Revolvers, UBSkidderz, Doubled AAL's, 3"SL/2"BL, winch/bumpers, skids, sliders, OBA, Snorkel, pine stripes....
Friends don't let friends drive stock.
http://www.gifsoup.com/view/501230/tj-tackling-crawlers-ridge-o.gif