I play against Baiken pretty much constantly, and I have noticed exactly one thing: All of her guard cancels are absolutely terrible if you're ready for them.
Against Baiken, going for block strings is going to get you hurt every time, whether by Sakura or sidestep-throw/combo. Your best bet, at least in the beginning, is to bait her into guard cancels. Any of Johnny's pokes can be used for this if you mist cancel properly, except perhaps 6HS or 6K. Generally, I've found it best to poke with 5k and 5HS to bait a counter. If she uses Sakura (that's the foreward-stab one) just block, then sweep. The same holds for the guard-cancel where she ducks down and throws a chain. If she has not RCed it when she sees you block, you're very likely to get a hit from at least the second hit of 2D. Sakura can be FRCed, but the FRC is late enough in the move that she will still probably eat the 2D
The hilarity comes when she does what I've noticed baiken does a lot, sidestep in an attempt to tick-throw or combo. A very good deal of the time, when she sidesteps she ends up *in* Johnny's character model, so if you're baiting it correctly it is a free throw.
Baiken also has a tendency to use Oren (The flippy air-move that hits you from behind), and you can bait this with coins if you dont mind getting a coin blocked once in a while. Simply, when you feel pretty certain that she is going to Oren when she blocks, you just toss a coin and instantly TK Ensega for a nasty counter-hit as her move starts.
It is very possible to win rounds against Baiken by simply baiting then countering her guard cancels, and Johnny for some reasons seems to be exceptionally good at this. Probably due to the range of his pokes. I wouldnt recommend trying to bait-counter for an entire match, as it will stop working once the Baiken player gets wary. Your best bet is to see what kind of guard cancels your particular Baiken likes to use, and then bait those particular moves mercilessly.
Not at all comprehensive, but what I've just said is an excellent way around those pesky guard-cancels. Best case scenario, you bait her all the way to a win. Worst case scenario? She just stops using them, which is also good for you.