okay my acoustic guitar pickup is the undersaddle type for some reason i can barely hear my D string while i can hear my other strings really clear

I suspect is because i always "shave" off the height of my saddle to my comfort and that might affect the pickup. Is there anyway to fix this? i tried adjusting the position of the pups but its still the same.

but i saw some pics on google that the pups are joined to the saddle. but mine has separated them

If your pickup is the under saddle transducer style, make certain that there's no debris hiding under it, between the pickup and the bottom of the saddle slot. A small bit of wood hiding in there is enough to disrupt the contact surfaces of these components. Also check that the saddle is fitting into the bridge slot nice and square so that the bottom surface of it is as flat as it can be against the top surface of the pickup. If your saddle piece is angled, it may not be in full contact with the pickup once tension is brought up on the strings. The string tension will tend to pull the saddle forward towards the neck so if it's not a snug square fit all around, you'll lose some energy from the strings going through the pickup.
If after checking all this you find that the D string is still completely dead through the amp, it could be a bad spot in the pickup in which case you'd have to replace it.
so i have to replace the pickup? and i just realized that as the string tension goes up i lost the sound. but as the string loosens up there's sound what do i do?
Well first, did you check that the saddle is square and seated properly like LeftyDave told you to do? You can't do anything with the strings still on the guitar, tight or loose
Quote by Captaincranky
Well first, did you check that the saddle is square and seated properly like LeftyDave told you to do? You can't do anything with the strings still on the guitar, tight or loose

what do you mean by "square"? but i do know that the saddle base is flat
i followed leftydave's advice on cleaning the pickups right now it has sound but still i can barely hear it
First check that the saddle is FULLY flat on the bottom. The way to check this is with a true straight edge. Lay the saddle bottom against the straight edge Don't push it on, as the saddle will bend toward straight. If you can see any light under the saddle, it's not straight.

As to "square", the bottom of the saddle must be at a true right angle, (90 degrees), to the sides. If it's less than 90 degrees, then the saddle won't make full contact with the transducer.

Your issue with string tension affecting sound seems like a saddle issue, but you could be a rare unlucky soul with a bad pickup.

If you don't understand the tools or terminology sufficiently, try to find a machinist or a woodworker to help you. A worker in either one of those trades would pick up these concepts immediately. Then of course there's the obvious take it to the music store. But, we'll try to get it working for free first.

This post may help you:
A good sandpaper for shaving a bridge is the same sticky back sandpaper used by body shops for their DA sanders. (The 80 grit takes stock off in a hurry, and then you can go to 180 or 220 grit for a fine finish). Get a nice piece of plate glass, at least 1/4" thick, put it on another flat surface, and don't grind off some stupid amount before you put it back in the guitar and try it, tuned up to pitch. Keep reversing the saddle, to avoid taking more off one end than the other, and block it against a 90 degree angle something or other, (called a "fence"), to keep the bottom at right angles to the sides. (I use a spare new saddle for the fence). Otherwise the saddle will lean funny in the bridge, and you may lose proper contact with the peizo. (If A/E)
Keep in mind we're not trying to lower the action of your guitar, but merely truing the saddle to mate properly with the peizo....

Hope this helps