How do you handle long runtime updates needed in hook_install()? I have a new module that includes a series of hook_update_N()s. I had written these without knowing that during module install the modules schema value is set to the highest value of hook_update_N() defined while the hook_update_N()s aren't actually run.

Several of the hook_update_N()s take advantage of $sandbox (Batch API), as they are lengthy database changes. As far as I know Batch API does not appear supported in hook_install().

What are my options to get these to run during module installation/deployment?
My suggestion is to not make it automatic on install. Provide a page from where an admin can launch the batch job.

However, if it absolutely must be automated, I have a suggestion, albeit a some what crude such:

hook_init() {
  $run_batch = variable_get('NOT_INSTALLED_YET', FALSE);
  if ($run_batch) {
    // Redirect to batch launch, or possible just set an approprite message.
  }
}

hook_install() {
  variable_set('NOT_INSTALLED_YET', TRUE);
}