I developed a multi-family prefab and it worked out well, but I had to compromise on a few things.

Upon visiting the manufacturing facility I realized I could never have the large ceiling heights I wanted, b/c each level is shipped on an 18 Wheeler and because of the low bridge heights, my desired ceiling height was cut down by a foot.

Pre-fab base finishes are bare bones, you'll want upgrades, from laminate crapola to higher end finishes like granite or hard wood.

Wen your levels are connected with large lag bolts or equivalent, there's obviously plumbing and electrical connections to worry about and then of course the inevitable landscaping that has to take place after construction is complete and if you're talking about Canada, you could be living with a nasty muddy frozen lawn with tire tracks all winter (snowy trip hazard :))

In any event, once you have your title insurance and taxes figured out, as well as architect, permits and fees, you should be good to go!

Good luck and btw RECORD THE PROCESS! Keepsake for the kids, a nice record for yourself etc. Nice to have, wish I recorded everything...

-Gregg