Starting timer jobs from Powershell is easy.Get the job, execute:
$webApp = Get-SPWebApplication "http://$($env:computername)/"
$job = $webApp.JobDefinitions | Where-Object { $_.Name -eq "<timer job name>"}
$job.Execute([System.Guid].GUID) # In my timer job I don't actually use the guid, so just create a new one
Write-Host "Done."
...mostly as a reminder to myself. :-)