my bad, amended instructions to remove the cover rather than the metal scuttle!
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I did mine last year. I’m only replying to confirm (as others have said) that the plastic scuttle cover has to come off to allow access (and the grommet cannot be removed through the hole in the cover). When in use, the cover is trying to pull the grommet out of the hole in the scuttle, so one wants the grommet pulled up as far as possible, giving the thickest possible layer of RTV underneath. I just squidged the silicone in whilst pulling the grommet up with its screw (really need 3 hands) until it stayed in place, then messily spread the silicone around to ensure a good seal, whilst not pushing down on the grommet. Slightly over-done, as this pic shows:
Have now done daughters MX5 also, adding silicone to new grommets with foam seals (mistake, too tight), may have to do again in 6 years.
NB pulling the old grommets out is hard and may (did in my case) bend the edges of the hole in the scuttle, no way I could see to help it out, as one cannot reach the inside part to squeeze the plastic ‘tongues’ together (but if one was really concerned, one could open up access inside the car and use pliers, but that might be tricky) - I couldn’t be bothered.
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Oddly enough I had to do the silicone sealant thing earlier in the week.
In the torrential rain on Tuesday I had to nip out to do a click and collect shopping run. The rain was hammering against the passenger side and as I started the car I spotted a single solitary drop of water into the passenger footwell.
The morning after I removed the scuttle cover, cleaned the area round the grommet and gunged it up as much as possible!
If that hasn’t fixed it, then I’ve a slightly more significant problem as the windscreen was replaced not long after I bought the car (errant stone on a dual carriageway to thank for that); it could potentially be the seal on the screen. I can always test that with washing up liquid or car soap though, by putting the fans on full - that blows bubbles where the air gets out 
Had the foam gasket failed?
It certainly had on my car. They are made of totally inadequate material.
Fingers crossed for you
Yep. Tiny bit of foam broke away when I ran my fingernail round it, so it got gunged.
Mazda were trying to defy logic with their grommet design. They should have inserted it from the bottom so the screw pulls the flange and gasket tighter agaiinst the underside of the metal scuttle…
For any long term owners it would probably be worth coating the screw threads with grease or vaseline etc as I would not want to try and drill a rusty screw out of that grommet the next time around
Or use a stainless screw
Be interested to know how the fix goes! I plan to do mine the same way as you one day next week - rather than trying to remove the screw and grommet I’ll just slap loads of sealant over them and hope that works!
When I did this with my old NC1 it worked perfectly. I did gently prise up the plastic surround and get some sealant underneath, but also made sure I got into the screw hole and all round the edges.
A bit rough but I’d rather it look a bit naff under the plastic and be dry, you know?
I just lifted mine and squeezed a neat bead underneath all the way round and it sealed just fine.
Sealed is sealed. The water is under no pressure
Most posts mention leak on passenger side, mine was on drivers side! Would suggest replacing both.
I bought replacement caps, grommets & washers from MX5Parts all for less than £10 including delivery (just to cover all eventualities whilst doing the job) I’m no mechanic & I completed the job in a morning including removing all parts including wipers & scuttle cover. WARNING! what took longest was removing the water from under the carpet & drying it out, I was amazed as to how much water had accumulated!
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