I was reading the D20 Modern system book, CyberScape, and saw an alternative application of cyberware described as magically animated material used as prosthetics.
I was wondering if there are any Shadowrun 4E rules anywhere allowing augmentation of mundanes using magical foci implants.
Another method would be to use a person’s body parts (tissue, organs, bones, etc.) as the bases for magical foci that confer physical or mental enhancements.
I know Adept powers are a kind of “magical augmentation”, but I am specifically asking for a direct replacement of normal (high-tech) augmentation for a mundane with some form of permanent magical augmentation.

I thank all in advance for any feedback and references.

Mundanes cannot bond Foci at all...
Maybe if you were using Unique Enchantements (Digital Grinoire).

You could get a spirit to possess your prosthetic (damn that's a hard word) limb I suppose

Only if you are adept at Calling and Negotiating. Maybe your Mage friend could do that for you, assuming he is a possession Tradition, but I do not think it works that way. Either an Object is possessed (At which point the Object benefits from the Spirit's Force (potentially)) or the Person himself is possessed, in which his body benefits, but is controlled by the spirit. Either way, the Mundane gets no real benefit from that arrangement.

Thanks for the reference to Digital Grimoire. It does indeed allow the possibility of using foci to permanently augment a mundane.
“…immediately bonds with anyone who holds it, magician or mundane, without having to pay Karma or perform a bonding ritual and they gain the benefit of the focus immediately.” – page 9

Now my next question is would such magical augmentation cost Essence? Is a “Mana-Borg” just as less human as a Cyborg? The rules would say that no Essence would be lost, if I read them correctly. If so, then I would imagine the big corps would be experimenting with such Mana-Tech.

This sounds like you are moving into Cyberzombie/mancy territory. What is it you are hoping to achieve? Most mundanes have no use for foci and weapon foci have to be an actual weapon. You can't get foci bonuses for unarmed combat. So cyber spurs as foci? You can already do that if you want.
Or are you trying to get all the benefits of cyberware without paying the cost? This is a cyberpunk genre game. Power is supposed to come with a price.

Spot on. Getting your arm chopped off and replaced with an artifical one costs Essence, regardless of whether the prosthesis is mechanical or magically animated.

The device described in the Grimoire is a unique item, and very powerful to boot. Seeing as anyone can use it, everyone would want it. You'd have to be some kind of nasty to hang on to it for any length of time.

Implants may not be as visible, but they would be as attractive. I don't see how an implant, even one made magical, would not cost Essence. Essence loss is about: having part of your whole self being replaced by something unnatural; mentally dealing with the loss of your person for power; buying into the addictive viscious circle of more, more, more.

Well... Clonal Parts do not cost essence. So, grow a clonal part (enchanting it as it grows, prior to implantation) and then implant it. *shrug*
Not something I would allow, personally, but that is a simple solution to the question of an Implant that costs no Essence...

Of course said part would have no enhancements beyond whatever the enchantment gave. What would you do? Quicken a bunch of Increase Attribute spells to it before implanting? Seems like you would be better off just quickening or anchoring those spells to you so they effect the whole body rather than just a part. Clonal parts are just replacements for what you already have. A clonal arm is no better than your regular arm, has no capacity and can't be modified in any way beyond what your regular could be.
I also would not allow this sort of thing in game. Like I said, seems more like someone is trying to step around the essence cost cyberware.

alternate solution:

step 1: augment character as per normal with cyber/bio/nano/gene/whatever-ware, following the exact same rules in every way.
step 2: say "it's magic" (making funny sounds and/or waving your hands around optional).
step 3: proceed to continue to treat it in every way the same as normal rules for non-magical versions of what the player has. every now and then, remind the player that it is, however, magical.

there you have it: magical enhancements for the mundane. problem solved.

Fixed.

Actually laughed out loud. Nice.