Lots of good advice. I did an 8k mile trip in 28 days with the wife, (Utah to Yukon/Alaska with a loop around Alaska) and we rode 200-400 mile days on average. I think your 21 days is fine for the trip you outline, but in the end, it depends on what you want to see and do. Of note is that both my wife and I ride our own bikes and we are both finishers in the Iron Butt Rally, (11k in 11 days). This trip was a vacation and we wanted to see/do things, not just hammer out miles. Some observations from a month on the road:
Plan some non-riding days into your trip. Seeing new things and riding miles is great, but at some point you will get weary of getting up, packing the bike and riding every single day. The down side to this is riding some longer days since your time line is fixed. You hopefully will have some points on your route that you want to spend more time exploring. Plan shorter riding days for the day you get to one of those spots, so that you can settle in and enjoy poking around in the afternoon/evening as well as the morning of the following day, (or the entire following day).
Reservations are good and bad. Good in that you know where you'll be stopping and you will have a room. Bad in that they tie you down to being in a specific spot that day. Being flexible is a good thing. Some of the spots we visited were worth every minute and we could have spent another day there. Others were a disappointment and we might as well have just spent a few hours there and not wasted an entire day stopped to see them.
Bigger/longer days will be a lot easier in the US than in Can. Especially as you move into the West towards the end of your trip. Finding a place to sleep at night will rarely be a problem on your Boston to Vancouver leg of the trip. However, you might check for events in areas that you believe you will be stopping for the dates you're likely to be there. Unknown festivals or sporting events can suck up every hotel room in a 100 mile radius for some events. Even in major cities in the West like Boise, ID.
If you're planning on having service done, make an appointment for first thing in the morning and specify that you will be on the road and waiting for the service to be done, and ask how long you should expect it to take. Plan on being there the night before so you can be certain to be at the shop when they open.
If you just want an oil/filter change, consider doing it in a parking lot, or bringing your own filter and having a quick lube place do it while you wait. Places like Jiffy lube will do oil changes on bikes if you ask, in most cases. I've done oil changes at a Walmart or similar big store by going in and buying an oil pan/jug, (the type that you can seal up when done), a funnel, oil and a filter, (or use the one I packed), and just finding an out of the way spot in the parking lot. After the oil change I take the container of old oil to the auto center at the store, or a quick lube place in the parking lot, or just leave the jug and funnel at a garbage can. Someone will snag the jug as a free item for them and all they have to do is dispose of the oil. Cost wise, it's more than the oil and filter would be for a change in the garage at home, but far less than the cost to pay someone else to do the job. FWIW, I've done this in the US and Can and never been hassled. I do go around back or the side where I am mostly out of sight of the bulk of customers and I don't leave a mess. Plan on having some latex/nitril gloves and some paper towels, (or just buy a roll at the store), to avoid you getting dirty or leaving a mess behind if you spill a little.
Tools - A good flat repair kit that you have actually used. And a small compressor that you have verified has the correct plug for your bike's power source that YOU installed. The oem cig plug outlet is not fused high enough for a compressor, and you should
not just install a higher rated fuse! It's simple to cut off the plug that came with it and install a new one if you already have a plug on the bike for a battery tender or heated gear. If you haven't done a flat repair on the road yet, when you next wear out a tire, use a small drill to make a hole in the tire and practice plugging it in the garage. That will at least give you some idea of what you're going to do on the road. On the road, it may be a jagged hole that has dirt or debris in it and it WILL need reaming before you can plug it. Make sure your kit has a reamer, and preferably T handles. And glue. Buy some fresh glue for the trip and extra sticky strings. If you have a Stop and Go kit, sell it to one of your friends that's not going on the trip with you and buy a good sticky string kit with T handles and a reamer, plus some extra sticky strings.. You can insert multiple sticky strings in a large hole and it will seal enough to get you to where you can buy a new tire. (I fixed a 10mm hole for a fellow on the Salmon Glacier road above Hyder, AK and he made it the 20k back down the gravel road to Hyder, and out to Smithers, BC the next day for a new tire w/o having to add air or it running low. It took 3 or 4 sticky strings.)
Have the tools to remove both wheels. Use them to do this before you leave. People forget about the 8mm allen bolt at the rear axle. You can get a new tire a lot quicker/cheaper if you pull the wheel yourself and walk it in from the parking lot. Not to mention that some non-Yamaha dealers won't touch your bike, but will still be happy to swap a tire out if the wheel is off the bike. For the front, you'll need something to prop up the bike, but that can be locally sourced, (rock, some wood, etc), or make a short prop from wood that you notch for your crash bar and can hold the front wheel off the ground with the bike on the center stand. (I've had both wheels off the bike at a dealer with this method w/o issue).
If you want to be free form on the ride, go for it. Stop when you see something you want to check out. But I would suggest that there is far more than you can possibly see on your trip and there will always be places that you wished you had spent more time at. Plan your route, then do some research about the places you believe you will be going. Every city or town has a web site or chamber of commerce site with "things to see and do" in their area.
Heated gear - Will you need it? Not absolutely. Will you use it and be more comfortable than w/o it if you have it along? Absolutely! I've had heated gear, currently only a Jacket liner, for over a decade. I ride 30-40k miles a year, all over the country. I've used the heated jacket liner in July, riding at night in the mountains of MT or UT or B.C. and in May, you can bet you're going to have some cool mornings where you've got the heated grips cranked up and are wishing you had a heated Jacket liner. A mounted Heat-troller from Warm-n-Safe costs a little more than the portable units, but being able to just pull the jacket liner out, put it on, then plug directly into the bike and ride off with the easy adjustment of the mounted knob is pretty wonderful.
Things to see - That's a tough one. Depends on what interests you. The wife and I spent an extra day in New York to see Niagara Falls, doing one of the tours so we could be off the bike and in street clothes. We enjoyed it and got to see and do more that way. The following day as we headed north we stopped at Old Fort Niagara and really enjoyed walking around and watching the re-enactments. She had never seen a black powder rifle fired before, or a cannon. They also have a very nice, small museum there that is worth the price of admission.
Find some place in Maine to have a good lobster meal. Maybe consider riding out to Perc'e Rock in Quebec and timing it so you can walk out at low tide.
http://en.wikipedia.org/wiki/Perc%C3%A9_Rock
Badlands National Park in South Dakota, (Wall Drug for sheer silliness too). Thousands of other places. Browse thru
Roadside America for fun and silly tourist attractions you might want to see. Go ride the Tail of the Dragon, just so you can tell people you did, and how incredibly boring it is, though with pretty scenery. Hit that mid week for any chance of riding it w/o stupid traffic and idiots. Take the hike around Devils Tower in Wyoming. It's an easy 30 minutes, even in full gear and quite worth it. Seek out some of the museums like the Henry Ford museum that are truly spectacular and plan on spending the day or half a day wandering around being inspired by the history and cool things to see.
You could do your same basic route 10 times and see all new stuff every time. You can't see it all, so pick what interests you and take notes during the trip of places or things you want to see the next time.
Have a great trip!