Symptom:
If you are getting a check engine light with a diagnostic code of P0410 (Secondary air injection system) most likely your secondary air injection one way valve is plugged up, the remedy is to replace the valve, and then reset the check engine light.  This DIY article describes how to replace the SAI one way valve.

Note:
The 99 model year 996 uses the same SAI one way valve as the 993, these valves are made by Nippondenso and are known to fail prematurely.  The 993 owners have been experiencing this failure on a regular basis, in addition to plugged air passage.   An updated combined valve and distributor housing was introduced on the 2000 model year (shop manual 26-30 page 4) and it is recommended in the shop manual when this valve need replacement to upgrade to the combine valve assembly.  I didn't bother with the update as I didn't want to update the entire manifold.  (save cost) 

Function of the Secondary air injection valve:
The Secondary air injection valve serves as an emission device, if the problem is not fixed it will not cause any running problem to the engine.  But in order to get your SMOG certificate the check engine light must be cleared, so the problem needs to be fixed.  There is a trick around the issue to get an SMOG certificate, which is to have the CEL reset and disconnect the battery immediately prior to a SMOG check, the SAI malfunction doesn't not trigger the check engine light on the first failure notice, instead I believe it is trigger on the 2nd accumulated error, so if you reset the code prior to SMOG you should be able to pass without any problem, but then the annoying check engine light would come on again later.

The SAI valve functions as a one way valve, which allows air to pass through the valve down stream into the air injection ports that goes to the exhaust manifold.  It's only functions is to dilute the rich cold engine start up air/fuel mixture in the first 15-30 seconds of a cold start up before it exits to the atmosphere, also provide extra oxygen to allow the catalytic converter to be more efficient during the cold start up.  installed immediately above the SAI valve is a check valve which is opened and closed by vacuum, when the SAI cycle is engaged the check valve is opened by the vacuum pressure to allow fresh air sent by the air pump to the SAI valve.  The nature of the one way SAI valve prevents hot exhaust gases from flowing in the reverse direction and send hot exhaust back up to the expensive electric air pump.  The check valve is an additional safety device to prevent the exhaust gas from going in reverse.  So typically if you have a blown open SAI valve the check valve is also burnt up, as that's the design intention to protect the air pump.

Removal procedures:

Disconnect the battery at the battery terminal. 

Unbolt the 13 mm air box bolt

Loosen the 7 mm intake hose strap

Pull the hose off the throttle body and lift the air box assembly up and tilt it so you can access the back side of the mass air flow sensor plug.  I found that just thumb pressure alone is not enough to unclip the plug to remove it, so you will have to use a small flat screw drive to pry the clip up in order to remove it.

Unplug the throttle position sensor on the throttle body and unbolt the four 13 mm throttle body bolts

Press the tab on the plug connection on top of the central intake distribution tube

Loosen the four 7 mm intake distribution tube strap and remove the intake distribution tube, there are two vacuum lines attached on the back of the intake distribution tube, take caution when removing the tube and tag the vacuum lines for assembly. 

Loosen the coolant drain hose connection bracket.  The shop manual calls to remove the hose, but I didn't find that procedure to be needed. 

Use a 27 mm socket to turn the belt tensioner clockwise to remove the belt.  Mark the travel direction of the belt as it needs to go back in the same direction.  Also remember the position of the belt arrangement, you might want to draw a picture to help you remember. 

Unplug the vacuum line on the electronic switch over valve (make sure you tag them as they get confusing later), unplug the electrical connection to the valve and remove the two 10 mm bolts holding the valve to the intake manifold.  I recommend removing this as it gives you more clearance to remove the alternator.

Remove the alternator idler pulley, and then the alternator bolt

Taking out the alternator maybe a little tough as it is wedged in the bracket pretty good.  Try to use a pry bar and lift it out of the right side bracket first and then over the lower mounting bolt bracket so that you can tilt the alternator forward to remove the electrical connection behind it.  There is one plug and one 13 mm bolt to remove in order to remove the main power connection.

Remove the rubber hose from the air pump to the check valve

Remove the electric change over valve on front of the SAI valve by unplug the electrical connector and pull out the two vacuum lines (Again you want to tag the vacuum lines for installation)

Now you will need a special tool to remove the SAI valve, you can use either a modified 27 mm craw foot, or a 1" craw foot widen and slimed down so it will fit beneath the SAI valve.  I had to remove the SAI valve with the check valve attached with the hose as one unit as the hose clamp was in a position where I couldn't get a good bite on it to loosen it. 

Most likely if you are getting a check engine light with an error code of P0410 you have a bad SAI valve, and depending on the fault condition of the SAI valve you may or may not need to replace the check valve.  You can check the function of the check valve by using a hand vacuum pump to activate the valve and try to blow air down stream and see if air gets passed.  If the valve opens with vacuum and closes without vacuum then it is still in good working order.

Installation notes:

Alternator - Once you wedge the alternator back in, mount the right side mounting bolt with the pulley idler first and then try to line it up with the left hand side bolt.

Intake distribution tube - Attach the two vacuum line to the back of the intake distribution tube first and then install the rubber sleeve on the intake runner on the left side first and the rubber sleeve on the distribution tube and then wedge the right side on first and then slide it all the way to the right and then the left side.  Do not tighten all 4 straps just yet.  You can tighten one strap on each side, as later you will need to adjust the intake distribution tube to line it up with the mounting position of the throttle body.

Throttle body adjustment - There is a bracket that mounts to the bottom left hand side of the throttle body bolt.  This bracket is used to determine the position of the throttle body, once the throttle body is secured then you can go ahead and tighten the rest of the intake distribution strap.