Killing hands don't do stun damage because they're magic, they do stun damage when you simply don't turn on the "killing bit" and are relying on a plain old meaty fist. When the magic is turned off and the meaty fist is filled with titanium, there is no room for stun damage as far as I can see it.

As a balance issue, I would simply never allow an attack to do physical and stun at the same time. If a sammy is punching people with a metal shock hand, I'd be giving the subject physical damage and some disorientation. Think it out. When I punch someone, I stun them and make them groggy (ie, stun damage). When I punch someone with knuckle dusters, I do serious physical damage that takes much longer to heal, but presumably I still stun them and make them groggy. Every physical attack realistically does something that would be counted as stun damage, but the game represents the stun as being included within the more serious physical damage track.

I hope not, because that would be silly. Increase strength from muscle replacement, and killing hands to do physical damage should stack to give more potent physical punches

Nope. Unless it is specifically stated as not being compatible, it normally is. Remember the long-standing, original tag line for Shadowrun ...

Where Man meets Magic and Machine

because strictly speaking that bio ini enhancer thingie is not TECHNOLOGICAL . . but BIOLOGICAL . .

Being biological doesn't stop it being technological. Scientific process and development lead to the design and implementation of bioware, so it's technological

Metal has nothing to do with technological.

To quote some definitions of technological

Bioware is clearly related to industrial and scientific progress, and is a most certainly a subject organised according to scientific principles.

Just because most of our visible technological advancement as a species has involved metals and machines, doesn't mean it's inherent in the definition

Which would be fine, except for the bit that explicitly states that Improved Reflexes can't be combined with magical or technological initiative boosters. It's not a limitation of magic vs technology, it's a limit inherent in that power. If the words were not written in to the definition of the power, then magic and technology would combine just fine

I'll leave aside the contentious issue of whether or not a cloned arm counts as technological under the game rules for this example, as it's not overly relevant in this instance. There is nothing in the killing hands description that says it's incompatible with technological body replacements etc. Technically, you could get a cyberarm and still use killing hands with it.

The reason the technological definition is relevant, is in the case of Improved Reflexes, which explicitly forbid combined usage with other magical or technological enhancements. Killing hands does not explicitly spell that limitation out.

I don't have the book with me, but I'm pretty sure both the cyberzombie and cyborg rules mention characters losing all of their magic/resonance when they go through either process.

Not the case at all. He can have faster reflexes. From one or the other source. They just aren't cumulative.

This smells of nitpicking. The point of the rule is to prevent unfairly achieving high power levels cheaply by combining several different weaker sources of enhancement. This is because initiative enhancers like Wired reflexes and Improved reflexes have escalating costs at higher levels. Combining the effect of Improved Reflexes and Synaptic boosters is as unfair as getting three instances of Wired Reflexes 1 installed in your body to get the effect of Wired 3. It'd be cheaper and cost less Essence. But it's an extreme violation of the intention of the rules.

I never said otherwise. I said as a matter of balance, I'd never allow it. I didn't say the rules don't allow it

Exactly why I have no problem with it.