Krug, let me see if I can step you through the differences between the 3.5 Rogue and the BCCS Thief.
First off, there are no alignments in the BCCS. Alignment is replaced by Allegiances, much like D20 Modern. Allegiances would be things like loyalty to a person, nation or city, organization, belief system, or an ethical or moral outlook. People with the same allegiances have a sort of bond. A +2 circumstance bonus on Charisma-based skill checks when dealing with someone with the same allegiance might be granted by the DM, as long as both parties involved are aware of the fact that they share an allegiance. PCs may start with up to three allegiances which are listed in order of most to least important, and which can be changed as they go along through life. A PC can start with no allegiances as well, such as a loner.
Second, the BCCS presents a "silver standard", meaning that silver coins are the normally used coinage. Gold coins exist but are rare and valuable. As a 3rd level character, you have 300 silver coins to spend on gear and anything left over 20 will be discarded so spend as much as possible. After going over your equipment list, I find that you only spent 55 silver and 2 copper, leaving you a total of 244 silver and 18 copper. If you would like to spend more, feel free. Or if based on Ratboy's background you would like to leave it as is, we can dump the excess and leave him with 20 silver to his name.
Your skills look good. All of them are class skills for the BCCS Thief or provided as class skills from the Beggar background, except Handle Animal as you have noted. It appears that you spent 70 skill points on skills. You should have a total of 60 points to spend for the Thief class by 3rd level plus the extra 4 points to spend on the background skills at 1st level and then 1 extra point per level to spend on those skills at 2nd and 3rd level. This would indicate a total of 66 skill points so you appear to be 4 points over. Someone else feel free to correct me if my math is off.
You are also entitled to one more feat. The one you have listed is from the Beggar background. You are also entitled to the free feat that all characters receive at 1st level. The Beggar feat acts as the bonus feat for being human.
Stats, saves, BAB, and that sort of data looks good.
Class abilities are all accurate.
Languages are quite a bit different than standard D&D. There are levels of fluency broken down into four levels, poor, fair, good, and mastery. Poor would be barely understanding simple words and mastery indicates a total mastery of the language. PCs begin play with fair fluency in their native tongue and a number of additional language points equal to their Int bonus. Each level of mastery of a language takes one language point. Each time a character buys one rank in Speak Language skill, that PC receives a number of language points equal to 1 + his Int bonus. These points must be spent immediately. Being able to read and write a language costs another language point and a PC is only as fluent with a written language as he is the spoken version. So in Ratboy's case, he gets fair fluency in his native tongue. He also has 2 more language points to spend based on his Int bonus. He could use those points to up his level of mastery in his native tongue from fair to mastery. Or he could buy poor mastery in two more languages, or he could upgrade his native from fair to good mastery and buy read and write in it as well. Hopefully these examples give you the general idea. Native language for Ratboy given his background would probably be Jewel Cities, which is the common tongue for many coastal cities on the Sea of Torments.
Hopefully this will allow you to complete the character. If you need any other questions answered, feel free to ask.
Toric