I noticed in Chummer it allows you to set "Do It Yourself" when putting together a deck during character creation, but I can't find the rules regarding this aside from talking about hardware tests after creation. Are there any requirements or penalties for putting a deck together yourself during creation?
There is no official rule about Build/Repair tests during chargen, but you don't need it to build a custom commlink
While building a commlink from scratch would require at least a shop to manufacture the plastic casing etc, you can buy a cheap commlink and improve it at will with hard and soft ware from the (black) market.
SR4A p.222 - Upgrading Devices:
If you are looking for more power in your device, you can upgrade its Matrix attributes. Upgrading a device is simply a matter of having the proper hardware module (for Response and Signal) or software package (for Firewall and System). Once you have the module or package, simply install it into the device, a matter of a few minutes’ work. A device’s ratings may only be upgraded by +2 with regards to their original ratings. Further improvements have no additional effect on performance. You do not have to upgrade all of a device’s attributes at once, even if the device has a Device Rating. In this case, the device can no longer be considered a “common” device, and should have its attributes recorded separately. A device may have only one hardware module or software package for each attribute. Rules for building your own modules or coding your own packages can be found on p. 228.
Remember that you can't buy anything at chargen with availability greater than 12 (SR4A p.86 - Gear), so if you look at the device upgrading table, you can't start the game with a response or a signal above rating 5. So you might want to start with buying a commlink with a rating 3 for those attributes, like a Novatech Airware (SR4A p.328).
Note: Runners's Companion offers a new quality, Restricted Gear, that allows to buy a piece of gear with an availability up to 20, for the minor cost of 5BP. You might want to look it up, but I'll assume for simplicity's sake that you won't take it.
You can then buy (SR4A p.330) and install your software on your custom Airware. Remember that your base Response limits your System, so you won't need to buy a System with a rating 6 right now (though you could, and gather enough money during runs to buy a Response-4 commlink and upgrade it to 6, so you wouldn't have to buy two Systems with different ratings.) System is also a limit to every program you commlink runs, so don't bother buying a Firewall with a rating greater than your response too.
So your commlink is a :
Novatech Airware (1.500¥)
Upgraded Response-5 (5.000¥)
Upgraded Signal-5 (1.000¥)
Custom System-5 (2.500¥)
Custom Firewall-5 (2.500¥)
And no skill test is even necessary.
Now, if you have some hardware skill and a very cooperative GM, you can propose a house-rule :
Using Building Hardware and Coding Software tables (SR4A p.228), you can get duration of an average extended test (with the buying hits rule, SR4A p.62), multiply it by the cost of a day (lifestyle divided by 30) and spend that much money. By no means it is an official rule, I'm just writing it here while I'm discussing DIY gear during chargen.
I'm not terribly familiar with Chummer, and I'm pretty sure Deckers aren't in 4th ed of Shadowrun but there are tables for setting up your Commlink in the core book. Presently I'm using the 20th Anniv. Corebook, which on pages 327-328 has the information you need to set up a Commlink which is essentially the Cyberdeck in 4e (nobody cough whilst saying "Smartphone").
The model of the commlink determines the Response and Signal where the OS determines the System (touched on page 222) and Firewall (A catch-all defensive stat). The extras in the Accessory table on 328 could fill in more of your DIY needs for extras.