i5 4460 & i5 4670K don't differ that much, though with a decent cooler you might as well go for the latter and overclock it.
Always nice to have a bit bigger SSD to run the non-vid media of off. 1TB HDD space is on the small side.
Really depends on what the difference in starting budget is and what you have to buy.
I have no idea what GPUs are usable for emulation and what platforms, but I guess:
i5 4670K / i5 4660 (stay away from stock coolers if possible)
16 GB RAM
MB with at least one x16 PCI-e slot. Preferably PCI-e 3.0
250GB SSD / 120GB SSD (120 is the absolute minimum / cheaper to add HDD space later down the line in general than buying a bigger SSD)
2-4 TB HDD space at least (no 3TB drives! / no Green drives! / 7200rpm / really depends on what systems you want, but space is easily added)
go to a PSU calculation site and see with all the parts need if 400 Watt is enough or if you should go for a 550 one. (preferably Gold rating, at least Bronze / don't go to near to the max capacity of the PSU for lifespan and efficiency)
Z87/Z97 is an overclock platform, H87 (as well as B ) is not.
memory clock really isn't that important.
If you buy 2nd hand, replace the cooling paste on the CPU.