Context. Temperature, surface gravity, and metallicitity are basic stellar atmospheric parameters necessary to characterize a star. There are several methods to derive these parameters and a comparison of their results often shows considerable discrepancies, even in the restricted group of solar-type FGK dwarfs. Aims: We want to check the differences in temperature between the standard spectroscopic technique based on iron lines and the infrared flux method (IRFM). We aim to improve the description of the spectroscopic temperatures especially for the cooler stars where the differences between the two methods are higher, as presented in a previous work. Methods: Our spectroscopic analysis was based on the iron excitation and ionization balance, assuming Kurucz model atmospheres in LTE. The abundance analysis was determined using the code MOOG. We optimized the line list using a cool star (HD 21749) with high resolution and high signal-to-noise spectrum, as a reference in order to check for weak, isolated lines. Results: We test the quality of the new line list by re-deriving stellar parameters for 451 stars with high resolution and signal-to-noise HARPS spectra, that were analyzed in a previous work with a larger line list. The comparison in temperatures between this work and the latest IRFM for the stars in common shows that the differences for the cooler stars are significantly smaller and more homogeneously distributed than in previous studies for stars with temperatures below 5000 K. Moreover, a comparison is presented between interferometric temperatures with our results that shows good agreement, even though the sample is small and the errors of the mean differences are large. We use the new line list to re-derive parameters for some of the cooler stars that host planets. Finally, we present the impact of the new temperatures on the [Cr i/Cr ii] and [Ti i/Ti ii] abundance ratios that previously showed systematic trends with temperature. We show that the slopes of these trends for the cooler stars become drastically smaller. Based on observations collected at the La Silla Paranal Observatory, ESO (Chile) with the HARPS spectrograph at the 3.6-m telescope (ESO runs ID 072.C-0488.Full Tables 2 and 3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/555/A150Appendix A is available in electronic form at http://www.aanda.org