The gene of interest is 3Kb long and I wonder if Taq Pol would be suitable for it as it can incorporate the wrong bases. Should I rather go with Pfu Polymerase?
For a 3kb DNA fragment, the usual Taq DNA polymerase will be sufficient (we have used it successfully). However, other proofreading polymerases for much longer sizes can be used including GoTaq® Hot Start Polymerase by Promega. Pfu polymerases are rather high-fidelity polymerases where extremely pure DNA is required for downstream application like cloning and mutagenesis