Is there somewhere to park the car at the border whilst we do all this paperwork?
Yes. You'll drive up to the US border officer and answer his questions. He'll direct you where to park - You follow his instructions and then go inside to fill out the paperwork. It will be straightforward.
If you want to receive brownie points, if you have power windows, when you pull up to the booth, wind down all the windows on the officer's side of the car so he can see in the back.
If the afternoon crossing is going to busy, should we just head to Seattle after the Boeing tour for a quick look around, have an early dinner and then head back from Seattle say around 6pm? or is this peak time?
If you have a phone with a browser you can check this web site:
http://www.cbsa-asfc.gc.ca/general/times/menu-e.html
You can also listen to AM 730 on the radio. Although this is a Vancouver station, you should receive it by Bellingham, Washington. They'll have regular border updates.
Please tell me it is not more hassle than worth to do a day trip from Vancouver to see the Boeing factory +/- Seattle
Certainly do-able, and many Vancouverites regularly do day-trips to Seattle. It's just important to note that since 9/11 crossing the border can be a time-consuming exercise. It could be a breeze, or could take 90 minutes - At a minimum allow for three hours in each direction.