First lets address the above:

Cyberdeck functionality, along with a hell of a lot of other stuff, was rolled into commlinks and they are relatively cheap.

Datajacks are most definately NOT things of the past, although people wearing 'trodes can now keep up to you the Datajack is still listed as equipment and people still have and use them.

Deckers are there too, I actually use the name often myself though I don't believe that the core book does anywhere. It has however become a more obscure idiom because the word that is the source of the name, "cyberdeck" or "deck", is nolonger in common use. I use the term for hackers that specializing in or at that momment acting towards Matrix entities, particularly VR, as opposed to vehicles.

Real physical connections with the Matrix still do exist. There are systems that, for whatever reason, do NOT have a direct wireless connection to the world/Matrix at large.

SOTA of has made him, like any other tech driven character, obsolete. He can go out and buy a functional commlink and a good spread of programs for startlingly less money than he had to lay out for his old deck.

There are character conversion rules for the Skills, but basically where he only needed one Skill before he now has 5 Skills.

There isn't really much in the way of canon implants currently that help him in VR anyway. Control Rig is pretty much it, and that is really a rigger item since it only helps you to control a vehicle you are jumped into.

That's really the crux of this, just like wide spread of computer applications with fairly user friendly built-in macroing, like Excel, lead to everyone and their dog a to claim to be computer programmer the increased accessablitiy and prevalence of Matrix use has blurred the line between decker and non-decker.

What Brahm said. Datajacks, headware memory (less so) and much decker-related cyberware is still in use. What has changed is the external hardware and software. A behind-SOTA decker is still using his 8-track when everyone has moved on to DVD. Even then there's still portions of the Matrix which use the old wired framework (some purposefully).

The update shouldn't be too much of an issue though, he can pick up a brand new commlink (replacing his cyberdeck) and suite of programs pretty cheaply (compared to SR3). Even assuming he's low on cash, getting the needed money from a loan shark or contact isn't beyond the realm of belief. On the plus side your decker is now capable of rigging (if he already wasn't) and may want to look into expanding his relevant skill set and gear.

You'll just need to convert your Skills and Atts to the new system (FanPro has a conversion guide on their webpage), shift some points around to balance the new Computer-related Skill Groups compared to the old single skill and you're ready to run.

Deckers/Hackers are actually one of the easier conversions to make.