Michael,
"My question is: Can I or do I sew the bottom and top extension collar on last, after I've sewn the main pack, turning it inside/out and sew the bottom, and then the top extension collar?"
Answer: Yes you can if you have free arm on your sewing machine for doing pant legs. It a pain especial with a pack bottom because the fabric is not as pliable the top is easier. You will sew a few inches stop the machine with the needle in the fabric then pull a couple of inches of fabric out from under the free arm and sew a couple of inches and repeat the process.
I have been finding out the less panels and seams you use on a pack design the lighter the pack is and stronger in construction keeping the fabric integrity. Here's some example of different pack builder way of making packs. You can make patterns for your pack on poster board.
If you have not cut the fabric out yet I have a plans for my nomad ruck that is stronger build with less seams.
http://www.backpackinglight.com/cgi-bin/backpackinglight/forums/thread_display.html?forum_thread_id=64282
Dave Chenault Black and White pack is also a good example of well designed pack with plans also he has photo sharing account link that show more photos.
http://www.backpackinglight.com/cgi-bin/backpackinglight/forums/thread_display.html?forum_thread_id=64995
Chris Zimmer also has some good photos of his wife pack. Chris Zimmer uses a one piece bath tub floor on his pack for less seams and stronger pack that can be adapted to your design.
http://www.backpackinglight.com/cgi-bin/backpackinglight/xdpy/forum_thread/52778/index.html?skip_to_post=445098#445098
If you have cut the fabric the more traditional way of sewing a four panel pack is to sew the bottom on to the sides/front of the pack and then sew the back on to to the pack.
Have fun,
Terry