I have twice canoed Spednic Lake and the St. Croix river to make a 50miler trip with some members of my Boy Scout troop...awesome trip and only one short portage and the fishing is great! I'll be doing this trip again in early August next year.
As for the Allagash, the best time is early June while there's still plenty of water runoff from the snow melt. After June things dry up a bit and make the portages a bit difficult. Of course the water's pretty damn cold in June.
I'm a bit weary of canoeing with just the wife, if you get mixed up and dump in some decent rapids you're without much help (even if the wife is an experienced paddler)
Two canoes and a group of 4 is much safer...don't forget, you can't simply call for help with your cell phone.
The Allagash to me is a lot more work than it's worth with so many better paddling choices, I'm not a fan of portaging canoes and all my gear, nor am I a fan of canoeing in shallows where it's almost better to hike.
Make sure you have some good dry-bags for gear, food clothes and sleeping bag, an Igloo Marine cooler or better (use block ice) Install tie-down points in your canoe and cover all your gear with a tarp, all tied in so when (not if) you dump your gear and canoe all stays together.
One of our guys dumped in some rapids on the St. Croix, the water pinned his canoe against a rock and nearly folded in half in about 5ft of water, I had to portage back upstream and paddle down to him. I exited my canoe and let it go downstream (other guys in the group grabbed it for me..we planned this) The two of us pryed and pulled for about half an hour trying to get the canoe unstuck while not getting washed down stream...we finally got it off the rock and floated downstream with it to calmer water.
If this ever happened to just 2 people in a canoe you'd be fucked.
Here are some ideas on what my scouts carry for a week long canoe trip;
Boy Scouts Canoe Trip Gear
ETA:
What brand / type canoe?
Here's a little write up of our last trip:
Spednic Lake, St. Croix River