a) About the first sentence, I think it's wrong to use sentence number one to mean what you mean. to play the electric guitar in the first sentence seems to be an independent infinitive clause. In other words, the better way (I think it still would be ambiguous) to write sentence number one is to put the last infinitive phrase at the beginning of the sentence.
To play the electric guitar, I don't use the same pick I use to play the acoustic guitar.
(Well ofcourse if you try to avoid the repetition too, your sentence'd sound better)
Plus I can see you're already aware of the fact that it seems weird if you use the infitive phrase in your sentence without an awkward pause that you try to show by a comma in your sentence. We don't use comma at the end of a sentence before an infinitive that concludes a main clause:
Main Clause + Ø + Infinitive Phrase. as in
Janice and her friends went to the mall to flirt with the cute guys.
That aside, whether you put a comma or you don't, you automatically make an ambiguous sentence by inserting the second infinitive phrase right after the other. Actually it's like you're making a series of and/or (or atleast they use comma for this). See this sentence as an instance.
I study my lessons every night to be a smart student, to make my parents happy, and/or to get good grades.
And if you don't use comma
I don't use the same pick I use to play the acoustic guitar to play the electric guitar.
it could mean that I don't use the same pick with the acoustic guitar so that I can play the electric one!
b) About the second sentence, when you say as I do you mean the whole structure that comes before it. So I think sentence two, although is a clear improvement compared to sentence one still bears an ambiguity. Actually your sentence could also mean that you don't repeatedly use just one special single pick to play the acoustic guitar (i.e. you change your pick regularly) while you use another single pick repeatedly to play the electric guitar (i.e. you don't change your pick).
I think you can say instead,
To play the acoustic guitar, I don't use the same pick(s) as the one(s) I do to play the electric guitar.
By the way I've tried to make the fewest changes as possible to your original sentences otherwise I think the sentences suggested in other answers are more appropriate and natural.