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1 My version of Haddock does not accept some infix operators like
(#)

In fact it does, but you have to add spaces between parentheses and the infix symbols sometimes:
( # )
.

2 How do I get hyperlinks to definitions in e.g. Haskell98?

You must have the relevant documentation installed e.g. ghc-doc. Then you can say e.g.:

haddock
    -odir=haddock --html
    --read-interface=http://www.haskell.org/ghc/docs/latest/html/libraries/base,/usr/share/doc/packages/ghc-doc/libraries/base/base.haddock
    --read-interface=http://www.haskell.org/ghc/docs/latest/html/libraries/haskell98,/usr/share/doc/packages/ghc-doc/libraries/haskell98/haskell98.haddock
    Data/LargeWord.hs

or much easier just use cabal:

./Setup haddock