There should already be drain holes in the sills located by each jacking point on the car (two each side).
The holes are in the welded seam along the bottom of the sill. Follow the sill along from each end and you will find a point that is wider than the rest of the seam. Use a small diameter drill bit to clean out the holes.
You should also clean out the drains from the corners of the hood fitting down through the bodywork. (One drain each side of the car that can only be found with the hood open) Be very gentle with either a trombone brush or just a length of curtain wire. Do not use a coat hanger as the drain pipe is in two parts and can be dislodged.
Just to make this clear the hood drains are two pipes that take rain water from the hood and feed it through to exits under the car.
If these drains are blocked the water will end up running into the car, maybe onto the floor but more likely into the sills.
Each sill has two small drains, front and back near the jacking points. These should also be kept clear.
As previously stated a curtain rod or trombone brush is ideal to clear the hood drains. I use a medium size cable tie to clear the sill drains which won’t remove paint or under seal from the sills. My first MX-5 suffered from the same tidal wave as you have experienced. On clearing the sill drains the water flowed for a good ten minutes.
Your car looks stunning. Hope we can help you keep it that way.
Contrary to some of the other suggestions i would not drill or use anything that would remove paint from the drain hoses, bare metal and water…rust!
Use something stiff and plastic, i use tie-wraps.
Thank you to everyone for your advice. I found the drain holes along the welded seam in the bottom of the sill. Took the advice and cleared them and the water came running out.
I found four drain holes in totals 2 on either side. Should there be anymore?
I have just checked my MK1 MX5, 1997 and can confirm that there should be 4 drain holes on each side. They are about 4 inches apart at each end on both sides of the two jacking points on the inner sill.
Sills should not fill with water. The only explanation for that happening is blocked roof drains. Hopefully those are now cleared and all water out of the sills.
Perhaps you may wish to invest in an endoscope that you can use with a smartphone to see inside the sills. You can never tell what has been done to a car in the past. Yeras ago it was a costly thing to do on a car but now it seems quite cheap.