What you're saying about uncertainty principle is strange. The principle says the longer the transition takes, the sharper the spectral line can be (but does not have to be, hence the inequality). There is nothing about uncertainty of measurement of time of some point event. The transition is not a point event. If the two states involved in the transition are known, then change of energy is known. How long the transition will take depends on strength and frequency characteristics of the external field, but the energy difference of energy of the molecule after the transition is over does not depend on that.