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1) Deckers are bloody expensive and unlike 4e hackers don't hybridize well. You can't really make a combat decker, instead the best you can do is a decker who isn't useless in a fight.
The only thing that is truly expensive about them is their deck. The difference between the Renraku Tsurugi at 214,000 and the Sony 720 at 345,000 is not worth the extra 130,000

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However, I think that the Tsurugi is about the lowest level deck you want if you want to be good at Decking. It also depends on what you mean by "useless in a fight" compared to "competent" compared to "combat decker"
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2) Resources come first because of how expensive everything is for a decker. This also leaves very little left over for augmentations that make you a good fighter. The best I can hope for is a competent fighter, not one that's actually good.
Resources A is necessary yes, given that you want both a good deck and augmentations. I disagree you can't make someone who is "actually good". Again, not sure what you are looking for as far as a "standard" samurai.
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3) Looking at the dice pools I probably won't hit much so suppressive fire is my only real offensive option.
I disagree, you have the opportunity to hit quite often.
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4) Automatics is the most versatile skill and I should take that as my weapon. Mainly because MPs and SMGs are one handed, full auto, and useful.
It depends on your GM, and the level of security you normally play with. I personally think Pistols is a better skill in some groups, but Automatics is incredibly versatile and never really a bad choice

With regards to you being "barely competent" perhaps you should describe what your GM normally throws at you in terms of opposition? If his standard goon is Reaction 6, Intuition 6, Wired 2, throwing 18 dice to shoot, then yes, you are barely competent.
But if you look at what should be a "standard opponent" i.e. Professional Rating 3 or 4, you are looking at them throwing 8 to 9 dice when shooting, and only dodging with 7 to 8 dice.
Now lets look at you, using Glyph's build for everything but what you chose to buy with the money:
With that 475K - you could look at:
Renraku Tsurugi - 214,000
Cyberarm 15000
Augmentation to Agility 6 - 15000
Agility Enhancement Rating 3 - 19500
Wired 1 - 39,000
Reflex Recorder - Automatics - 14,000
Cerebral Booster 2 - 63000
Reaction Enhancer 1 - 13000
Datajack - 1000
Cybereyes Rating 2 - 6000
(inside eyes) Smartlink - 4000
Lowlight 1500
Thermo 1500
This still leaves you with @70,000 for armor, programs, weapons, lifestyle, equipment, etc.
Using Glyph's character sheet with these changes, it makes your stats:
Body: 3
Agility: 2 [9]
Reaction: 3 (6)
Strength: 2
Charisma: 2
Intuition: 4
Logic: 6 (8 )
Willpower: 5
Edge: 5
I would also take away the Pilot Ground Craft, and pump another point into Automatics and Stealth:
So now you are looking at rolling:
Agility 9
Skill 5
Specialization 2
Smartgun Link 2
Reflex Recorder 1
Or a total of 19 dice.
This still leaves you with @70,000 for armor, programs, weapons, lifestyle, equipment, etc.
Your Initiative goes up to 2d6+10
Your dodge is still 10 dice
Will you be able to use the variety of weapons a Samurai can? No. Will you be as physically competent as a Samurai? No. But you can be
really effective in a gun-fight, as well as being an excellent decker. And the Samurai can't do
anything in the realm of the Matrix that you can do.
And that isn't a bad thing - if you could be every bit as good a Samurai as someone who didn't want to be a Samurai/Decker, that would be sort of silly, wouldn't it?
My 2 cents anyways.