Let me assume that initial velocity & radius are Vi and Ri. & the final velcity and radius are Vf and Rf .
Since u pull the string and hence the force and radius vector are along the same line therefore no net torque acts on the system and hence angular momentum is conserved. Thus equation 2 must be used.
It is possible to pull the string in such a way that the initial and final tensions remain the same. In such a case both equations 1) and 2) are to be used and hence the values of Rf and Vf are fixed (meaning: u cannot choose the Rf and the fact that tension remains the same. Choosing one automatically determines the other.)
Out of the manny possible ways in which the radius can be reduced one of them is the way in which the tension of the string remains the same.
Ur equation 3) is completely wrong and hence cannot be used. The reason is that the radius cannot be reduced without a spiral motion. In this case we seem to simplify the problem and take into account the initial and final states only. When u apply the extra tension to the body directed to the centre u set it in motion along the radius. Now by conservation of linear momentum along the radius how can u explain its abrupt stopping at the desired radial distance. Obviously a retarding force must act in the direction of the radius to bring the body to a stop. This complicates the situation and hence work energy theorem cannot be applied with the simplification u seek.