From a chemistry background, your choice of allergy makes my brain hurt. Ya, I know, MAGIC! But its just that gold is so inert and nigh impossible to get it to react with anything that I can't figure out how you can be allergic to it.
Pretty much it's RAR MAGIC! Heck back in the 1st edition days, metahumans got a randomly determined allergy and gold was one of the possible substances, just like wood, silver, or sunlight.
As for the characters, let me start by saying that you have a good start. He's competent at being a street samurai and would take him over a sample character any day. But let's see if we can make him better. I will only look at the core book for now.
First off, let's look at your skills. You have a bunch of skills at 3. As rasmusnicolj said, the most karma efficient way is to have skills at 4. So I would move your skills around. I would drop Climbing, Dodge, and Running. I would buy the Athletics Group at 1. This saves you 24BP. Instead of dodge, you'll use gymnastics (not that I recommend active defenses). As for climbing and running, there's ware that helps with that. You also are better at swimming for what that's worth.
With the 24BP, I'll raise your infilitration and perception to 4, leaving you with 16BP spare. Both are very handy skills. You could drop both and grab the Stealth group at 4 instead. You'll need to buy up perception during play, but you'll also be okay at disguise and shadowing (especially if you buy up your Int).
Now you're at a crossroads when it comes to armorer and first aid. You're good enough to be meh at this stuff. While you can put a smartlink on a gun by yourself, you don't need armorer for much else in core. With
Arsenal, you have gun mod options which you are okay or very meh at depending on how you do extended tests. However you could also just pay someone to do this stuff. As for first aid, you can roll 12 dice (with medkit) which isn't that much better than the 9 you'll be rolling without any skill.
So you have two options. One is to drop the armorer and first aid skills, lower your logic to 2 (you can go down to 1) and move the 34 BP elsewhere. You'll need people to mod your guns and you'll be better off handing your med kit to someone else, but that's some deep point savings. If you know your team has a high logic type, I would recommend going this route. The logic guy can handle the modding and first aiding. In a pinch, you can first aid with 8 dice (likely spend a point of edge if you can).
The other option is to be the logic type and make the most of it. I would consider this if no one else is a logic character or you expect to be alone a lot. Being an ork stinks for logic, but the point savings elsewhere are worth the effective -1 logic.
Augmentation has a lot of options to help you out if you go this route.
Since you'll be sneaking around a lot, being able to bypass maglocks is really really handy. Therefore, the hardware skill can pay off. Buy up your logic to 4 and get hardware 4. Buy some cerebral boosters 2 and you now have a 10 dice hardware check. That'll cover most maglocks and give you a decent chance at anti-tamper systems. After that, buy up your first aid to 4*. That will cost you 30BP from what you have now. I'll buy down armorer to 1 to save on points. Depending on how much you have to spare, you might want to pick up mechanics so you can be good at modding cars, but that can also wait for karma.
Speaking of karma, it is usually better to buy specializations in play rather than at creation. Since you're mundane, spending karma for specialization is a good idea since you don't have to save for initiation like awakened or technomacners. You'll rather have the 6BP now than 6 karma later. I would recommend grabbing hardware (maglocks), first aid (combat wounds), armorer (weapon modification) if you go the logic path.
As for attributes, they are mostly fine. I would lower your strength to 5 as All4BigGuns points out. I would move that point into Int or Logic (if you're going the logic route). If you're dropping logic instead, I'll also consider increasing reaction to 5 as well. Willpower 3 is acceptable though I wish there was a way to get it to 5 without too much dumpstating but I don't think there is.
I would drop toughness and pain resistance. Pain don't hurt in SR4. As for toughness, you're going to be fairly tough anyways. I'll move the 25 BP elsewhere.
Now it's time for your gear. Convert whatever spare BP you have from the work above into cash. If you need more cash, I'll see what else can be cut. I think you can spend the full 250,000Y of starting nuyen even with just the core books.
You have the right idea that as a mundane, the state of your soul doesn't matter and you can walk around with essence of .3. However, I'll find ways to make your soul stretch further. Muscle replacement uses up to much essence for its cost. I would instead get muscle toner 2 and muscle augmentation 2 for 30,000Y (net cost: 10000Y). Then I'll remove your dermal plating for now and downgrade your wired reflexes to basic grade. This give you a total savings of 42000Y and an essence of 2.55. Eventually you'll want to buy muscle toner 4 and muscle augmentation 4.
I would then get a Synthacardium 3 for 30,000Y. Your new superheart gives you +3 to your athletics skills so overall you're just as skilled in those fields as before but you saved 18BP and are good at swimming. I'll also grab reaction enhancers 2 for 20000Y. That'll put you at a 8 reaction which is pretty keen. You'll now be at 1.8 essence.
If you're going the logic route, you'll want to buy cerebral boosters 2. Other that, you can pick up nifty ware. Ones that are nice are platelet factories, enhanced articulation, or dermal plating.
As for weapons, you're right that the Alpha is the best gun. I'm not sure how you're getting 6 RC though. With gas vent 3 + innate 2, you should have 5. Does Chummer use the strength adds to recoil compensation rule by default? Either way, be sure to add a shock pad for an additional 1 point of RC.
As for your concealable backup, the Black Scorpion is fine. I like the TMP more since full-auto wide bursts are sometimes handy. You might want to look into the HK-227X since it has restricted legality suppressed fire. That or get a sound suppressed Alpha for when you need to be quiet.
Now for melee, things get more interesting. Right now, you're going with the blades approach. I would be sure to get a knife or some other sort of concealed bladed weapon. The reason why is that if you have a blade out, you can use your blade skill in melee defensive tests. That saves you the need to have a dodge skill (and one of the reasons I suggested dropping it earlier). You might also want to consider getting a spur installed. It's like having a sword on command. However its illegality makes it a debatable choice.
You could also go the Unarmed route. Being unarmed means you'll always have unarmed added to your melee defense. There's also some good unarmed options. One is to use a shock glove. That doesn't play to your strength score however. You can also get bone lacing and have your unbreakable bones do extra damage. Sadly it's also forbidden legality. Either way is fine, but I thought you might want to know your options.
In a later post, I'll discuss what in
Augmentation and
Arsenal you should get or consider. There's some gems in both books. Overall,
Augmentation has some ways to make you tougher and helps a lot if you're going the logic path.
Arsenal will make you much tougher stackable armor and deadly due to better recoil compensation options.
