An essential part of looking after your MX-5 (Mk 1 to Mk 3.5, and I guess Mk 4 too?) is to keep the internal roof drains running freely. A blockage will mean your boot will get wet, as will the footwells under the seats.

Trombone cleaners SHOULD NOT BE USED! If you have gotten one stuck, this video includes a tip which may help you get it out.