[Suicide Junkie]

As for #1, that is a limitation in SE4...
Maximum 255 points, after which it wraps around to 0 again.

Basically, think of it as the maximum engines the ship can support...
If you really need to go faster, use a smaller hull (less mass means the same thrust(#engines) moves it faster)

#3 Is, I believe, a family number problem. Hitting upgrade makes it use the ship yard instead of the base yard or vice versa.