Did you check the pulse hose for a loose fit on the carb and base? Sounds like it's not getting a strong enough pulse, also take the hose off and just slip a little screw driver in there to make sure it is not plugged up at all. Also, you should really consider looking into upgrading from the 38mm Keihin to a Mikuni SBN44 and carb adapter. Those Westcoast pipes are quite a bit larger on the I.D. compared to the stock chamber and I found the 38 Keihin was not enough carb to satisfy the airflow demands of any modded or AM pipe. Another area that is known to be problematic on the 650sx engine over time is the case drain plug. It's on the bottom of the exhaust side of the cases and has that little pull plunger mounted on top of the exhaust manifold. If they start to leak then you won't get much pulse signal if any at all as all the signal will be going through the case drains. There is a very effective and affordable fix for those drains, don't use a block-off plate, they leak fairly soon after the first season or two. Just coat a pair of stainless bolts (1/2-13 if I remember correctly) with JB cold weld and thread them in. Don't tap the holes, they are just the right size that the bolts will do it with no troubles. If you tap the holes, the chips from the tapping will get sent into the base where they will make bad things happen. Just driving the bolts in by the ratchet works the same as a roll tap, it forms the threads in accordance to the constant spiral of the pitch. Regular taps are fluted where the chips buildup and break off rather then mold with the pitch.
*Edit*
Also wanted to add that the crank seals should be replaced if they have never been done that you know of. Most people don't change them since those engines are quite bullet proof and rarely need any large scale maintenance. Crank seals that are 25 years old have served their purpose and are most likely soft opening up air gaps between the seal and crank. If you block the exhaust manifold with a good sealed and bolted on plate, then pressurize the cases through the pulse fitting, they should hold about 15psi if the seals are good. If not, no amount of carb work and swapping out will get that engine running or running well...if air is entering the system from anywhere below the bottom flange of the carb (intake gasket leaks, base gasket leaks, crank seal leaks) the engine will be a carburetion nightmare.
