The feasibility pump took longer to get an incumbent than your first run did (and got a worse incumbent), so I would turn that off again.
Changes to the presolve options resulted in a larger problem (more rows, more columns, more nonzeros), which might or might not pay for itself in terms of a tighter bound. The root relaxation solutions time went up from 181 seconds to 246 seconds, indicating the larger model is more difficult to solve even as an LP. What really stands out, though, is that once CPLEX starts branching your node throughput is much lower. In your first run, CPLEX is averaging around 0.3 seconds per node. In your second run, it is around 6.6 seconds per node.
So, in addition to getting rid of the feasibility pump, I would suggest removing the HeurFreq, CutPass and Probe settings, and see if the throughput picks up again. If it does, you can try adding those settings one at a time and see if they help.
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