Good idea with sticking to 5.56 for now - you can always change uppers later as time and money and availability improve. 1:9 is fine for the 5.56, gives you a range of 52gr through upper 60 grains, like 67 or something like that. You just can't use the "heavy" 70 gr and higher weight bullets.
I have a Stag upper, and it is very nice. Can't go wrong with Stag. I remember MB talking a couple years ago about shooting a Stag rifle out of the box, no cleaning or anything, and was shooting tight groups, and the gun ran flawlessly.
Go with a flat top, Tom, you can always get a removable carry handle if you decide you want one. I have a DPMS with the handle permanently mounted, wish I had the flattop. The handle screws with optics mounts rather badly. Even with a Z-mount for the optics on the handle, they are way high for me.