Don't be too concerned about removing the ship. It's in there tight, but with a bit of jigging around, it can be done - see LTG's previous post on page 64 of this thread.
For me, putting it back in place was more difficult. What seemed to work best was pushing the front end just under the ramp first, and then wiggling it around until the bracket with the 'male' end engaged with the 'female' bracket standup thingy on the playfield. It was easy to see when it had engaged, as the ship pivoted left and right in a controlled way when I moved it with my hand. Then it was just a case of putting the allen-type screw back in on the back of the ship, and the washer/pin behind the playfield.
I'll be better at it next time (although I'm hoping nothing else will go wrong under there), and there will be less swearing/sweating.
Addition: while you've got the ship off, I suggest you check whether the wiring loom is too tight. Mine was, and I snipped a couple of wire-ties to loosen it. Hopefully the wires won't get in the path of the ball when it enters the lanes below the ship, but I'll post here if that happens. Best of luck!