We report the first comparisons of pickup proton simulation results with in-situ measurements of pickup protons obtained by the SWICS instrument on Ulysses. Simulations were run using the three dimensional (3D) time-dependent Hybrid Heliospheric Modeling System with Pickup Protons (HHMS-PI) (Detman, et al., 2011). HHMS-PI is an MHD solar wind model, expanded to include the basic physics of pickup protons from neutral hydrogen that drifts into the heliosphere from the local interstellar medium. We use the same model and input data developed by Detman et al. (2011) to now investigate the pickup protons. The simulated interval of 82 days in 2003-2004, includes both quiet solar wind (SW) and also the October-November 2003 solar events (the "Halloween 2003" solar storms). The HHMS-PI pickup proton simulations generally agree with the SWICS measurements and the HHMS-PI simulated solar wind generally agrees with Ulysses SWOOPS measurements. Many specific features in the observations are well represented by the model. We simulated twenty specific solar events associated with the Halloween 2003 storm. We give the specific values of the solar input parameters for the HHMS-PI simulations that provide the best combined agreement in the times of arrival of the solar-generated shocks at both ACE and Ulysses. We show graphical comparisons of simulated and observed parameters, and give quantitative measures of the agreement of simulated with observed parameters. We suggest that some of the variations in the pickup proton density during the Halloween 2003 solar events may be attributed to depletion of the inflowing local interstellar medium neutral hydrogen caused by its increased conversion to pickup protons in the immediately preceding shock.