It sounds like some part of the charging system has had it, I think what you are seeing is that when the bike is cold (i.e. battery has been doing nothing for a while) you have no probs but after a run (life sucked out of battery as it's not being charged) the electrics are giving you grief.
The easiest way to test goes as follows, but you will need either a multimeter or could get away with a bulb and a wire. Disconnect the regulator, and check for continuity between the three wires in three pairs, i.e. pick any two and check current flows down one and back up the other, repeat for the other two combinations. You should have continuity (a few ohms resistance). Check for continuity between each wire and earth (the engine or frame will do) - there shold be no current flow. If both these tests are okay then the stator coils should be fine, but to confirm you would need to measure the voltage across pairs of wires with the engine running (>75V at 5000rpm is usual). Really if the resistance tests pass then it will be the regulator, these days they should last for ever so I would just get another Suzuki one, it's not the 70s/80s any more thank God.
If the stator coils are knackered then it could be that the regulator has gone and therefore burned out the stator. You can test it but you need a resistance table, should be in the manual. Don't assume that there is only one fault.
New stator should be around the £30-40 mark, try Electrex near Reading or West Country Windings.
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