I am sure you will have many answers for enzymes but one problem is the high GC content. Running any pcr in presence of 1 Molar betaine is very helpful in making the melting of the high GC template much easier and making the pcr work with any polymerase
Th phusion Taq includes a buffer that goes well for high GC content, and also is a high fidelity enzyme, that it would be more suitable for cloning after amplification