Acoustic Guitar pickup sound loss

I'm sure that you did a careful and a pristine and accurate job.

Judging from the instructions below, I see only 2 things that could have gone wrong to affect your acoustic sound, namely the direct transfer of vibration through the saddle from the strings, cleanly and without a break (no air or space) to the bottom of the bridge route, which is still a factory component. You want total contact, even with the under-saddle pickup inbetween.

Number 1, did you drill out, or countersink the main hole through which the pickup element was passed? That must be done to allow the whole pickup to sit perfectly flat, not only to prevent pinching of the wire.

Secondly, and finally, all that I could speculate is that the bottom of the factory route wasn't flat or smooth in the bridge, as the instructions suggest. Check it and scrape it with snapped-off Olfa or box cutter blades.

This was from the company's instructions, sorry that pictures would not copy. The saddle should sit as upright as possible under string tension, thus you angled the bottom in the opposite direction of the leaning-tendency, and as you said kept it flat.

"Inspect the inside of the guitar and note the position of the braces in relation
to the saddle slot. Drill at either end of the slot on the side that will enable
you to avoid all braces as you penetrate the top, as shown in figure 5. Blow out
the slot with compressed air and check for remaining debris.
Important: Round the inside of the hole where it meets the bottom of the slot
with a small, sharp knife or small file to avoid pinching the pickup as the
saddle lies on it.
Feed the pickup into the slot from inside the guitar with either side up.
Inserting a toothpick or similar object through the hole from the outside is
helpful in finding the location of the hole on the inside of the guitar.
Important: The fit of the saddle in the slot is the single most important factor
in this installation. It is crucial that the bottom of the slot and the lower
surface of the saddle be flat to make even contact with the pickup. The saddle
should fit loosely enough in the slot that it can be pulled out with your
fingertips. It will then have a slight forward lean when the strings are under
tension. It is absolutely necessary to compensate for this slight lean by
sanding a tilt in the bottom of the saddle so it still sits flat on the pickup when
the strings are at tension (see figure 6). If the saddle is too tight, binds at all or
is too loose, this will have a negative effect on the string balance and output.
Insert the saddle in the slot and note how much material must be removed to
compensate for the thickness of the pickup. Remove the saddle and sand its
bottom surface on a belt sander until the scribe line is just above the bridge
top. Finish sanding the bottom by hand. It is best to do this against a
machined flat surface with fine sandpaper. Use a straight edge with a strong
light source to inspect the flatness of your saddle.
Insert the pickup all the way into the slot, place the saddle on top of it, and
temporarily secure it with a piece of tape. Secure the wire with a wire clip as
close to the exit hole as is practical, with a one- to two-inch service loop.
Failure to secure the wire may produce boominess and feedback. Now restring
the guitar, plug the pickup wire into the preamp's left-hand socket, and plug
into your amp or PA. Confirm that the EQ controls are at their default positions
and test the Element, paying careful attention to string balance. If the sound is
satisfactory, the installation is complete. If not, read on.
String balance problems are almost always the result of an uneven interface
between the bottom of the saddle and the saddle slot. If the string balance is
uneven, check these surfaces to ensure that they are both completely flat.
Tip: A segmented packaging knife blade is a useful tool in determining the
flatness of the saddle slot. Break off only enough blade segments so as much
blade fits into the slot as possible. Briefly use a back-and-forth scraping
motion to see if the slot bottom scrapes evenly. Any high or low spots will be
readily apparent. A minor low spot in the slot may be compensated for by
shims under the pickup; however, for gaps over .005" or multiple gaps, we
recommend rerouting the slot."

You could virtually do what it says in the last sentence by scraping cleanly and precisely from end to end in the saddle route with the appropriate sized jeweller's screwdriver.

I appreciate your need to hurry and resolve the problem. I have done this before, and hope it helps. :)