...can it be done in a 16' aluminum canoe at 260 CFS? or will I be dragging my craft through the rocks?

All depends on what you mean by the lower Stilly. Arlington to I-5 has a few shallow places, notably just above the cement plant. Below I-5, the Pilchuck Creek channel (go right just above the dam) usually has enough water to get you down to where the channels come back together below Silvana. Below that point you get into the tidal zone and how much depth you'll have depends on the stage of the tide (usually enough though). Below I-5 the bottom is largely sand and gravel so dragging isn't too much of a problem. Arlington to Blue Stilly Park is a reasonable float, and you can stretch it out a bit by continuing down the Pilchuck channel to Pilchuck Creek and up the creek to take out at the bridge. Blue Stilly Park or Pilchuck bridge to the Bodel Bridge boat launch (on the Warm Beach-Stanwood highway) is a pretty long float, but do-able in a day. With a canoe you can probably portage around the dam and take the left-hand channel down to the Town Tavern at Silvana (a rough take out), there is also a rough take-out right under I-5.

Thanks for the info! I think I'll go do some scouting around before I try it though...