As a new player to Ars Magica 5th edition I have a couple of questions.
In previous editions there were rules for laboratory customization, in the grimoire. Are there current rules concerning laboratory customization or are the 4th ed rules still good??
How does one determine the number of botch die to role? I've been over the 5th ed main rule book and haven't been able to locate specifics.
Thank you for any information you may have to contribute.
Angado of Cymril of the Seven Kingdoms 
Hi and welcome to 5th edition!
Rules for laboratory customization can be found in Covenants. You could probably convert the 4th ed. rules without much trouble though.
Botch dice are very much the same as prior editions but here are the guidelines.
Stress die: base 1 botch die
Abilities: If you do not have the ability at all, add 3 botch dice
Lab Experimentation: Add risk modifier in botch dice
Vis: Add a botch die for every pawn of vis involved
Aura: add number of botch dice equal level of foreign aura
Regio: Double the number of botch dice (this is after adding for foreign aura)
Cautious sorcerer: subtract 3 botch dice down to minimum of 1
Familiar: Subtract Golden cord rating from magic (lab and casting) botch dice
Lab Safety: Add or subtract your lab safety rating from number of botch dice while working in lab (min 1)
Spell Mastery: Subtract your mastery score from number of botch dice
There is also a modifier for boundaries of magic realm but I am not sure what they are off hand.
I think covers most cases.
I haven't read Covenants, so I wondering about this "foreign" aura note. I am assuming a Magic aura is not foreign to magi, but other types are. Would a Faerie aura still be "foreign" to a Merinita (or any mage for that matter who has the Faerie magic virtue)?
No, the Faerie Magic Virtue attunes you to both realms. There are similar Virtues for other realms.
Foreign aura. For most mages, Divine, Faerie and infernal are the foreign auras that in a Faerie aura 5, +5 botch dice. If it is a Faerie regio 5 then +11 botch dice (1+5 then doubled to 12 or 11 more than original).
Faerie magic attunes you that faerie is no longer a foreign aura. Holy Magic attunes that Divine is no longer foreign aura, I am sure there is one for infernal but I don't know it off hand.
Chthonic Magic.
Guilty as charged Mr. Quaesitor. Now let's see you make it to Tribunal...
I know. It is just that I have been delving into the potentials and possibilities for Chthonic magic, as it pertains to my villan character Metron. That is some insidous $#!+ right there, I tell you what! 
Here's a whole load of my personal opinion on the subject of botch dice. You should feel no obligation to pay it much mind, if you've played prior editions it's probably nothing new to you.
The specifics are on the bottom of page 7 of the core book, middle column,
The game absolutely would not benefit from too many more specifics beyond this. (Not to imply that a paragraph like ladyphoenix's post wouldn't have been a good inclusion.)
Everything else in the rules that specifies botch dice is just an expansion of this paragraph. It really is up to the storyguide.
Sticking with the climbing the cliff example additional botch dice could be appropriate
if it is dark
if it is raining
if people are shooting arrows at the climber
if the climber is drunk
If the cliff is as reflective as a mirror
If the cliff is covered with oil
If the climber is covered in pudding
If the area is experiencing an earthquake
If there are stoats in the climber's tunic
If the climber has sand in his eyes as a result of a cruel creo terram spell
If there are an abundance of mountain goats on the cliff with the climber
If the climber is injured
If the climber is exceedingly nauseous
and so on and so on
You don't want to put this sort of a thing in rules that are more detailed than the paragraph on page 7. You end up with more confusion, less fun and less verisimilitude.
Craft sex Chtonic toys? 
Xavi
Oh, man, I hate it when that happens! That's the worst, no doubt!
The stoats are dangerous for sure. I always add a couple botch dice when stoats are present. And newts. Newts are dangerous as well.
Xavi
She turned you into a newt ?!?
... ... I got better...
It ws like curse of Circe, duration sun.
Actually that is what I thought when I read Curse of Circe for the first time. 
Xavi
You always get a few more botch dice if it would be horribly embarassing for you to fail. Such as if your parens is watching you perform at Tribunal.
"- Look! It's my boy up there!
thank you all for your comments. That actually helped quite a lot.