I recommend the GTX 750 or 750ti as the step up in terms of GPU.
About the M.2. ....
Yes you are right that the board only has x2 not x4 and your SSD would certainly be constrained by an x2 M.2 slot. However, it would still be extremely fast (faster than a SATA III based SSD) even over just two lanes, so it is really about what you are doing. In normal use you won't notice ANY difference whatsover between x2 and x4. Only if you tested it within a very specific and demanding high end application which it seems like you will never need.
Nevertheless, if you really still need the x4, there are some limited options for you. My opinion is 'do you
really need that extra performance for home use??
If yes, then you can either:
1) Get a board with an ultra m.2 slot such as the ASROCK EXTREME 6 Z97
PCPartPicker part list /
Price breakdown by merchant
Motherboard: ASRock Z97 Extreme6/ac ATX LGA1150 Motherboard ($158.29 @ Newegg)
Total: $158.29
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2015-01-23 12:35 EST-0500
or 2) Buy one of these http://rog.asus.com/327432014/labels/product-news/asus-hyper-m-2-x4-pci-express-gen23-to-m-2-x4-ssd-adapter-card/.
In my personal opinion I think the cost is not worth the performance and especially for you (where the system is already overkill and m.2 is already SO fast). I think you should stick with the ASUS Z97 PRO with the x2 slot. You really won't notice the difference.