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I have to cast my vote with urging you to stick with the Shadowrun system. I've played both from their inceptions, and the systems are tuned well to their respective genres. Pathfinder characters are high-fantasy heroic, able to shrug off massive wounds and keep fighting to the end. Wizards are like gods to the man on the street, and the actual gods will bend the rules to keep great heroes alive. The rules support this well (well, fairly well).
Shadowrun, though, is necessarily different. Fights are brutal and fatal. Wounds HURT, and magic is taxing and can turn on you. The system helps to support this feeling of desperation and menace.
Years ago, I surprised my 2e campaign players by dropping them (via gate) into the Shadowrun world. I converted all their characters over a weekend, and the next session, I just started off with exposition. They were in an abandoned warehouse that had huge holes in its walls. Several bodies were seen huddled around the open room, snoring. When the party paladin approached one, he was shocked to find an orc. All of a sudden, a noise like a swarm of angry dire wasps was heard from outside. The orc squatters all panicked and tried to run, as a band of cybered-up bodyjackers crashed the squat, looking to take a few captives. The paladin (a bit of a swashbuckler) leapt to the defense of one of them, yelling something like, "Unhand that man!"
At which point the bodyjacker looked at him, sneered, and unloaded half-a-clip of SMG fire into his stomach. I handed them their new character sheets, gave them a second, then said, "You just took 9 boxes of physical trauma. Welcome to the Death Spiral."
They treated Seattle like a g+~%!#n warzone after that.
Shadowrun might have magic, but it is a cyberpunk game at heart. The ruleset for Pathfinder just doesn't fit.