When they first leave the ship.... in San Francisco, they walk off/down the stairs/lift of the ship... we see the stair rails But the ship is cloaked!

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    It's a stolen ship, they probably didn't know how to re adjust the cloaking field. – user16696 Mar 15 '15 at 23:36

The cloaking field seems to extend around the normal extent of the ship. When objects protrude from this silhouette, they become visible. This is explicitly confirmed in the movie's novelisation:

For a minute Javy considered jumping out of the truck, but Ben had it going nearly fifty. Javy tried to see behind them in the side mirror, but the light and the ramp had vanished, and he could make out only shadows.

Jim led the way out of the Bounty and signaled for the ramp to withdraw. It disappeared into the cloaking field. The hatch closed, cutting off the interior light. Star Trek IV : Novelisation

We see another example of this when Scotty sticks the upper half of his body outside the field when he's manhandling the plexiglass walls into place:

Gillian gasped. The man hung unsupported in the air. But from the waist down, he did not even exist. It was as if he were standing within a structure that could not be seen and that could conceal him as well. An invisible structure ... "

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    @Thepopmachine - No. They pay for the perspex by giving the engineer the formula for transparent aluminium. – Valorum Mar 16 '15 at 18:37
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    @ThePopMachine - From the novelisation "Ah, what else indeed? Let me put it another way. How thick would ye need to make a sheet of your acrylic"-Scott hesitated a moment, converting meters to feet, wishing the twentieth century had finished getting around to the change--"sixty feet by ten feet, if ye wished it to withstand the pressure o’ 18,000 cubic feet 0' water?". "That's easy," Nichols said. "Six inches. We carry stuff that big in stock." – Valorum Mar 16 '15 at 19:20
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    @ThePopMachine - And from the script; SCOTT: Ah, what else indeed? I'll put it another way. How thick would a piece of your plexiglass need to be, at sixty feet by ten feet to withstand the pressure of eighteen thousand cubic feet of water? NICHOLS: That's easy, six inches. We carry stuff that big in stock. – Valorum Mar 16 '15 at 19:22
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    @ThePopMachine - From the novelisation; "In the far end of the cargo bay, the water nearly reached the top of the acrylic tank" – Valorum Mar 16 '15 at 19:38
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    @ThePopMachine - And from the script; "Cut to : The Plexicorp helicopter, carrying an enormous pane of plexiglass across the city. It is not exactly steady." – Valorum Mar 16 '15 at 19:40

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