Looks like a pretty good start (well triangulated, susp points would be near existing nodes, drivetrain and driver space is ample), but yeah, building around (even roughly decided) suspension points and engine/diff/driver models is much more efficient. I know dpcars has r1 block and a good editable driver model you could tweak to your dimensions, but I don't know much about importing to sketchup as SW is my medium of choice. :\
By the looks of it, you could slim the front and rear sections considerably (that pedal area is kinda awkward imo, and keeping the top tubes all even has little benefit aside from easier jigs/fixtures, both can be tapered to fit the driver and drivetrain, gain rigidity and drop a few lb), but as it's still essentially a blank slate this is relatively easy to play with as you go through suspension design and frame validation (FEA). The braces (longitudinal and X) over the cockpit don't seem to add to strength notably, and could be dropped altogether... though you could retain the X-brace between the roll hoop and front, but put raise the center of the X (so it's 4 tubes instead of 2 and points up a bit), which will give you a bit of extra knee/foot space. Your front roll hoop should ideally be one tube from the top of the cockpit, to the bottom frame rails on both sides with no 'breaks' in the line, though using multiple tubes is fine too, as long as it still looks like one hoop. You'd need to bring those 2 vertical tubes forward a bit, which I'd recommend anyway for comfort/space. Formula SAE is an excellent resource here for design and packaging ideas, there's a number of frame design papers packed with data and countless images to run through for ideas on packaging the parts neatly and creatively.
I'll just make a note that some of the miata parts are better replaced by scaled-down components suited to the role, but that's down to your budget and design. You'll have a tricky time trying to cram an OEM steering rack into that car without some major modification and potential bump steer problems, whereas a small rack would open your options considerably. The brakes will be overkill as well, but as they fit nicely, packaging is not an issue with miata uprights, and you know they'll work well enough, I don't see the harm. What are your plans/ideas for the suspension, and how are you mounting the diff?
There's an awful lot to consider in 1-seater frame design aside from maximum rigidity for minimum weight. Ergonomics/driver fit and comfort (egress rules/goals? these tend to be very snug and awkward, a cardboard/pvc mockup is a great idea), serviceability (does the engine/diff drop out, are there braces in its path that can be bolted in/out or adjusted to fit?), handling the torque from the drivetrain, as well as hanging all the important bits on it (shocks, diff, radiator) that may or may not contribute some load themselves. Of course, much of this can be guesstimated and sorted out on the shop floor with varying, but typically mediocre results, but IMO if 3 hours of CAD time can save me 1 hour of frustrating wheel-spinning during a build and produce a higher-quality result, I'll take it. Details and refinement (thought-out designs, not complexity) make all the difference in a car like this, I'd say you're off to a fine start thus far. 
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I think you'd be up against an absolute brick wall trying to get a car like that street-legal. Not that any one element may be illegal, but you'll need to fit a body, lights, potentially bumpers, fenders, and depending on laws where you live, any number (0-inf) of rules to comply with meant for normal cars, and be hard-pressed to find an inspector who would ok a tiny, short-wheelbase, bike engined, open wheeled single seater that wraps around the driver like a glove as he sits an inch off the ground, staring at everyone's tires. It's possible (anything is with enough money and stubbornness), but the amount of effort and fighting that's likely to take could be much better spent driving it as a strictly track/auto-x car, IMO.