So I've been agonizing over the Matrix in my SWN to Shadowrun conversion.
Today I realized that there are perfectly serviceable rules for hacking in the SWN supplement, Polychrome. They are not as robust or complex as the SR Matrix rules, but they are simple as hell and allow the hacker (though I still prefer the term decker) to work in real-time with the team. If hacking is done on-site, it takes only 1d6 rounds... some of the things a hacker can do are quite analogous to the D&D thief, which was the sweet spot I was going for.
I think I will put my Matrix system on the shelf and simply say that if I run Shadowrun with SWN, I am going to be using those hacking rules instead.
Now, I just need cyberware and beasties and I think I have enough to run. Polychrome also solved my Wired Reflexes problem in an very elegant way: each round a character uses super reflexes, they get a second action at the end of the round. (There is essentially an extra "round" at the end of the round for wired characters) Using your wires causes a point of System Strain each time you use them, and you have to make a Tech Save or else they overheat and shut off for one hour. Perhaps you could include advanced levels of it that don't overheat, but still cause the Strain... something to simulate Wired 2 and Wired 3 without turning your game into a slogfest.