Here's my reading of this:

Except Party X, which is still led by Y, all the parties now have new chairmen, who, however, remain close allies of the influential party figures.

I suppose that people wanted to see a shakeup that would bring new blood to the leadership of the parties. However, the new party chairmen are very much attached to the same people who have held the real power all along.
Is this interpretation correct?

And yes, 'ally' is used within the context of political parties.


--------------------------------------------------
Note added at 13 hrs 19 mins (2005-07-15 12:19:07 GMT)
--------------------------------------------------

BBC examples:
Of the nine men now on China\'s most powerful political body, six are close allies of Mr Jiang.
As recently as Thursday of last week, close allies of the Health Secretary insisted he would not run for the job of mayor.
All three ministers belong to the BJP. Mr Mahojan and Mr Malhotra are close allies of Mr Vajpayee.
CNN examples:
The 59-year-old Hu will now head a so-called \'Fourth Generation\' nine-member leadership body stacked with close allies of his predecessor.
Khalil and Ghani were once close allies of ousted deputy prime minister Anwar Ibrahim

Problems with the grammar of the original:
‘except’ is better that ‘except for’ in this case.
A comma before ‘which’ for this non-defining clause.
You can’t use ‘almost’ if you have mentioned ‘except’.
‘now have new chairmen’ or ‘have now elected new chairmen’: Do NOT use the present continuous with ‘have’ in this case.
I prefer ‘who, however, …’ because it creates a direct link which eliminates any doubts as to who ‘they’ are.
‘are close allies OF’ (plural) or ‘closely allied TO/WITH’ (as suggested by Andrew)