How do you hold the plectrum? The best way to hold it is between your thumb and the side of the index finger (beyond the last knuckle) where your index finger basically points in the direction of the tip of the plectrum. The gentlest of pressures will keep the pick in place.
If you hold it between the tips of your index finger and thumb you will stress the last joint on your finger which is possibly why your finger aches.
As for your thumb pain while barring chords, are you sure you're not applying excessive pressure? The string only needs to touch the fret not the fretboard. So fretting as close to the actual fret as possible will reduce the pressure you have to apply.
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