It looks like a simple grammar so I'd use a recursive descent parser, Parse::RecDescent for one.
This is just a example off the top of my head and completely untested.
start : '(' section(s) ')'
section : '(' id entry(s) ')'
entry : '(' section | keypair ')'
keypair : '(' key value ')'
Update
Looking at this again, entry shouldn't have those terminal brackets -- it would only parse sections like '(id ((key value))', so just
entry : section | keypair
(I did say this was just off the top of my head !)
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