Yeah, virtual machines for legacy gaming haven't really panned out either.
Yes, I should have upgraded to the GTX 950. This is the first time I've built a computer in about 8 years, so I've been a bit oblivious to trends.
My only advice would be to buy a graphics card, in whatever price range. That would make the biggest difference compared to running everything on the APU. I'm also not sure what operating system you are using but that would also make a difference.
I would also say that you could stick with 4 GB RAM instead of 6 GB. It's always possible to upgrade down the road but that amount of memory would probably not be noticeable . That's one way to save $16.