Absolutely, it's a great idea! I bought my carbon Fuji that way. It was 2009, they stopped making them in 2008, sold out of my size in the 2008, but there was a 2007 with a nearly-identical spec sitting in a warehouse. Never been unpacked, built, nothing....winner!

I prefer building my own bikes from the frame up. That way, I get to spec every single part to exactly my needs. No take-offs, upgrades, nothing....just my perfect bike. I enjoy the wrenching part too

If it were me, I'd go to the shop sometime when you know they won't be busy (not Saturday ), and have a good chat with your favorite mechanic or mech-savvy salesperson about parts that fit your budget and riding style. Maybe even ride a few bikes with different parts just to see what you like, especially if you don't already have some strong preferences for certain components.

As for wheels, I like reliable handbuilts....no bling, but durable, light, and easy to get replacement spokes for. Proprietary spokes make me batty.

Have fun with it!!