MK3 or MK3.5 for 'racing'

nc1 5spd is pretty decent, fairly long gear spacing, would suit a turbo, if you are stripping out and kitting out, then a non sport 5spd in a nice starting point, no ac, no fancy stuff just barebones 5. I prefer the 5spd for low speed events like solos the first is longish and it'll drop from 2nd to 1st with ease, the 6spd can be reluctant.

3.5 sport has better engine and at some stage an improved 6spd gearbox. (might have been at 3.75) but comes with additional stuff that adds weight and probably don't need like leather/ac/heated seats etc, nicer looking car though, the extra gear is nice, it breaks up the long 3rd, the 5spd 4.1 diff goes well with the 6spd to make gearing even snappier.

3.5 has less chance of being a rusty prarrie canoeter to.

But any 5 will get the job done, I went for the cheapest battered NC1 5spd I could find and saved my dough, had some fun in it with the mx5 challenge and then did some  updates to it that ended up costing more than the car as is my penchant for not leaving well enough alone  

It will make no difference which mx5 you get, just set your budget and get cracking, you might find that as its end of season some cars are up for sale already prepped but if you want to enter some of the entrt level mx5 specific classes you need to be wary of what has been done as it might exclude you.