Mazda hesitates majorly

My Mazda Protégé 2000, 1.6 litres (manual) has recently been starting up very rough and when this happens the car is almost unable to be driven as it hesitates majorly, compromising speed and power. However this behaviour doesn't happen every time it is driven, so it has really got me puzzled!
When affected the car takes unreasonable time to increase speed, even though the accelerator is pushed to full capacity. When the car is required to come to a stop, it would eventually stall when the brakes are applied unless the clutch is ridden to keep up the revs.
As said earlier, the interesting thing about this case is the car is not affected all the time. I noticed that it is more likely to 'play up’ when the car has recently been driven (i.E. Warm).
Please help

Steve