Corrected entry: At the start, Captain Janeway reveals that she has discovered Tuvok's birthday. Then she says it's not long before he hits the big 3-digits (meaning 100 years old). However, Tuvok was 107 when he infiltrated the Maquis and they've already spent 6 years on Voyager. Even if she didn't discover his birth year and was only guessing. Tuvok would not have replied with "indeed" but pointed out she is wrong.
Corrected entry: What happened to the Type-9 shuttle that was given to Kes in "The Gift?" She could have crashed this into Voyager just as well and she could still have transported aboard as the shuttle has a transporter.
Correction: Federation shuttles wouldn't be able to keep up with Federation starships so she probably traded it in and used local starships to catch up to Voyager. She then acquired the shuttle she was in when she caught up with Voyager.
Kes has the ability to destroy and kill with a thought and can time travel at will. I'm pretty sure she wouldn't need a fast ship to catch Voyager. Using a ship to ram Voyager was probably just a distraction/up yours to Janeway. We can be pretty sure that the Type-9 shuttle she left in was destroyed during her transformation.
Correction: We don't know whether they are speaking in terms of Earth years or Vulcan years.