BG 2 I have noticed is a mixture of 2nd and 3rd edition rules, which is insanity in and of itself. If you plan on running a game based on those rules, I wish you luck. That's crazy.
As far as dice rolling programs, I posted this in the "What Can Change A Man" thread, but go here:
Dice Bag :: d20srd.org. It isn't perfect, but it's a ready made dice rolling program. Just a note, again, if you plan on using DnD, you really won't want to base it off of BG2, as they're rule system is wonky and I am honestly wondering how in all hell they set up a mix of 2nd and 3rd edition DnD. They are completely incompatible.
I would suggest learning the rules on the
The Hypertext d20 SRD (v3.5 d20 System Reference Document) :: d20srd.org website first. Perhaps joining in a game with someone who has played to learn with them and have someone who knows the rules teach you as you play.
Then again, people do learn on their own in groups where no one knows. So, if you want to do that, good for you. Maybe it will work out, and you will like it.
As far as Time Stop, time stop didn't exist in 2nd Edition I don't believe, or if it did, it worked different. Why? Because 2nd edition was made under a different ruleset, by different people who worked for a different owner/company. Comparing that website to BG is not going to work. Ignore BG and read the website like a text book. The rules are all there, you just need to absorb them and apply them.
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SO i cannot argue on that, but i thought the game designers followed core rules. So i took BG2 as s representation of 2n ed rules. Actually since you seem to have the resources could you check how did Time Stop work in 2nd ed rules, because i found this information: 
Linear Mode
