Talk to some local builders. One thing you'll probably discover is that you can build much cheaper than buying an existing home.
For example, we built our 3500sqft home in the Smokies for ~$285/sqft. Good luck buying a cabin for that price now. (We're custom building another now.)
As for the mortgage, one option is a construction loan. We started by buying the lot with cash and owning it outright. Then the loan required 20% down but the land value counted. In our case, the lot was 20% of the construction cost so we didn't need to put any more cash down. The loan had a one time closing fee and after construction was complete converted into a 30 year mortgage.
Be careful on the mortgage because ours is a 5 year ARM. But we plan on having it paid off in 5 years so it doesn't matter. You can find construction loans with standard 30 year mortgages.
During the construction process, the builder sends invoices to the bank to cover current costs and asks you to approve and then cuts a check to the builder. This process continues until the construction completes.
As for architect, be prepared to pay 10 - 25k depending on the size of the property. In our case, it was an investment that was well worth it ($25k plan for a $1mil property that we absolutely love).
Focus your energy on vetting the builder. I've heard so many horror stories about builders being late, delivering the wrong floorplans, shoddy work, etc. This is the greatest risk in custom construction.