Smartlink: Check out the errata:
http://old.shadowrun4.com/resources/errata_mm.shtml
p. 32 Smartlink Subsystem Game Effects [3]
Change the remarks in parentheses, found in the second paragraph, to read:
"(any non-implant substitutions are made)"
So your reading is correct, but you're safe.
Chemicals: Chemicals delivered how you describe. However, wound modifiers from a knife wound do NOT apply to resisting damage from chemicals (SR3 p. 126 lists what wound modifiers apply to, and specify it does not apply to resisting or avoiding damage).
Gun-knife: I said we could work something out on this. I'll do some research and come up with a model. Expect that it won't be as effective at gunning or knifing as a dedicated tool.
Magic Rising: There are some SR3R rules for this. I'll need to read through them and get back to you.
Pulling Punches: Martial Arts maneuvers frustrate me, because they're for martial arts, but nothing else. I would like to either drop martial arts maneuvers as its own category of rules, or get a list of maneuvers for other combat styles. In general, if I "drop" them, that doesn't mean that they aren't available for use. Pulling punches is a thing, whether you're trained in boxing or not. I'd use the maneuver rules as guidelines, and tweak them as appropriate. (Expect it will never be easier than the rules described. How much harder depends on what the maneuver is. Any idiot can pull punches, but sweeping or ground-fighting are very tough.)
I would like some thoughts on the Martial Arts maneuvers from people (and also the magic, once I come back with something).
I'll put out a Players Wanted ad today.