With difficult templates, things are just you know.. difficult
Actually kits are you know, for that kind of use, when you just want to simply clone your fragment, because your real aim is not cloning or learning how to became a superskilled bacteria guy, but when you want a result as fast an comfortable as possible.
That's why I use the best PCR master mix available, because I make new PCR reactions like every other week and I just don't want to spend my time optimizing something I may run 10 times at all. It's different if you want to make a super cheap optimzed reaction for screening or routine something. It's just that optimizing PCRs is not your research aim, PCR is just a way how to get there. Same is for cloning, if it's not some hardcore construct preparation, when you need half a year of no results to get the mad skills.
Of course relying solely on kits is stupid, you need to read the kit, understand how it works and at what cases it won't work and see if it's even suitable fo you. Kits are comfortable but they are not no-brainers. You still need to think and understand it to work with it.
I don't think you only have option to stupidly mix kits and if they don't work then stare into the walls or do everything the "right" harder, classic way. You should be able to do both and able to decide when to use what (by the way I woudn't buy the same kit if it failed once.. at least Invitrogen has Zero brand of vectors, that minimize false positives, if nothing, but given your high GC product.. I would suspect it to make problems and try to find something about it before trying new kit, I like kits but I care about the money as well )