The CO Mapping Array Project (COMAP) Pathfinder is performing line intensity mapping of CO emission to trace the distribution of unresolved galaxies at redshift z ∼ 3. We present an improved version of the COMAP data processing pipeline and apply it to the first two Seasons of observations. This analysis improves on the COMAP Early Science (ES) results in several key aspects. On the observational side, all second season scans were made in constant-elevation mode, after noting that the previous Lissajous scans were associated with increased systematic errors; those scans accounted for 50% of the total Season 1 data volume. In addition, all new observations were restricted to an elevation range of 35–65 degrees to minimize sidelobe ground pickup. On the data processing side, more effective data cleaning in both the time and map domain allowed us to eliminate all data-driven power spectrum-based cuts. This increases the overall data retention and reduces the risk of signal subtraction bias. However, due to the increased sensitivity, two new pointing-correlated systematic errors have emerged, and we introduced a new map-domain PCA filter to suppress these errors. Subtracting only five out of 256 PCA modes, we find that the standard deviation of the cleaned maps decreases by 67% on large angular scales, and after applying this filter, the maps appear consistent with instrumental noise. Combining all of these improvements, we find that each hour of raw Season 2 observations yields on average 3.2 times more cleaned data compared to the ES analysis. Combining this with the increase in raw observational hours, the effective amount of data available for high-level analysis is a factor of eight higher than in the ES analysis. The resulting maps have reached an uncertainty of 25–50 μK per voxel, providing by far the strongest constraints on cosmological CO line emission published to date.