The prices listed in SR4A are specifically for upgrade modules. As Bradd points out, they (and the 100¥ cheap case) don't include:
The motherboard
The power supply
Any buswork which is not part of the buswork
And those three items are, practically speaking, what limits your ability to upgrade, as represented by the +2 cap on upgrading gear.
As a GM, I'm going to let you build your own comm-link, but it's not going to be as simple / cheap as buying an empty case and upgrade parts intended for hot-swapping into existing commlinks.
I might (it's counter productive to the megas to make building your own commlink cheap or easy) let you buy a "bare-bones" (That's case + MoBo + PS + Buswork) with a pre-defined upgrade limit. Otherwise, you'll either need to harvest parts from an existing commlink, build your barebones system from scratch, or lift a bare-bones system during a run against an electronics manufacturing plant.
All this puts us heavily in the "what your GM allows" territory.
If a GM wanted to be a jerk, he could point out that an empty case has a Device Rating of 0, and thus was limited in accepting upgrades to 2/2. Heck, I could see the AAA's even doing whatever it took to ensure that this was the limit of the private consumer's ability to make their own commlinks. Guarantees that the hobbyist electrician gets laughed at by their consumerist friends.
Maybe I'm missing something, but reading over "The Wireless World" in SR4A, particularly the sections on upgrading and using the hardware skill, "Using Technical Skills to Build or Repair" on page 138 of SR4A, and going through Unwired, I can't find any RAW that supports build-from-scratch commlinks except for the very GM Fiat heavy "Using Technical Skills to Build or Repair" rules.