I do not understand your choices
The pre-1994 NA 1.6's have very weak rear differentials and drive shafts, not a great base for turbo'ing. Also the short nose block is something I would avoid.
Also not sure about the AC either, do you really need it in The Netherlands? Creates a mess under the hood and makes cooling more difficult. Miata's are terrible when it comes to cooling, turbo'ing makes things worse.
Also w.r.t. rust: did you check the sills properly? Only checking the wheel arches seems silly to me.
Only getting 100 euros off without MoT / APK is a bit stupid in my opinion. There could be a whole myriad of problems in that car to get it through. The rough running and the seller not wanting to put a new APK on it tells me enough. Also all the buttons and weird gadgets that have been bodged in does not give me confidence in the previous owners. I would have walked away...
The only thing I like is the fact they used a toilet refresher under the hood near the brake booster
BTW, where are you located in The Netherlands? I live near Utrecht and will be picking up my MX-5 project again soon. Maybe we can do some collaboration?