You will need to buy a new saddle and install it or have it installed. You should probably pay a professional guitar technician to do a full setup on the guitar to correct the problems.
If your high and low E strings no longer touch the saddle, it is a certainty that these strings will not play in tune at any fret position.
Moreover, to correct the initial problem, you should not have focused all your attentions on the saddle. The nut, the truss rod (an adjustable steel rod inside the neck which can be used to introduce or adjust a slight amount of bow into the neck -- the fingerboard is not supposed to be totally straight and flat. Adjusting the truss rod correctly is essential for proper string height and intonation and to prevent notes from buzzing, among other things.), and the saddle all most likely need to be adjusted together and interactively to correct these kinds of problems. In extreme conditions, the neck has settled into the wrong angle to the guitar body, and in those cases the entire neck has to be removed and then re-glued back in place at a different angle to correct the problem. This is called a neck reset, and it's an expensive proposition. If you are faced with the need for a neck reset, you might decide to buy a new guitar instead.
Also, a careful truss rod adjustment may be needed if your guitar goes through significant changes in temperature or humidity. This is a necessary part of regular maintenance. The wood of the instrument will expand or contract with changes in the climate, and the neck may increase or decrease its amount of bow under the tension of the strings. In some geographic locations just the annual change of the seasons can throw the neck out of alignment, requiring occasional truss rod adjustment. If your guitar is old or new but it has not had truss rod adjustments, I guarantee that this will be required right now to get your guitar playing properly again.
Initially, the top surface of the saddle needs to be carefully shaped to have the same curvature (radius) as that of the fingerboard on your guitar. This needs to be done by using precise measuring equipment, and a special calibrated sanding jig, which a professional guitar technician will have. If your saddle was initially carved to the correct curvature, but you altered it by sanding off the top surface of the saddle indiscriminately, or you sanded off too much on the bottom of the saddle, well, that's a problem.
As you have already discovered, these kinds of adjustments need to be done incrementally and carefully. You should have removed just a little bit of saddle material, then re-installed the saddle and re-strung the guitar to see if the situation had improved, and if not, then removed everything, pulled out the saddle, and adjusted things a tiny bit more, then repeat the whole process. The best thing would have been to have precise measuring devices and understanding how to use them so you could predict the outcome before you sanded away too much material.
Save yourself further grief and pay a professional whatever is necessary to correct all these problems, with a new saddle, the labor necessary to shape it properly, a full setup on all the other relevant parts of the guitar, and of course a new set of strings. Just take the guitar to a qualified repair person, and ask them to give it a quick visual inspection and to tell you approximately how much money it will cost to get everything fixed correctly. You will probably need to spend anywhere from US $75 upwards, depending on how much work needs to be done.
Here is a 30-minute video from Premier Guitar Magazine in the USA, showing the steps involved in shaping a bridge saddle for an acoustic guitar.
However, the video does not cover truss rod adjustment, nut adjustment, dressing frets, and other elements of a full setup.
There are myriad videos on YouTube explaining the concept of acoustic guitar neck truss rod adjustment.
If you want to learn more about what it takes to do a full setup on an acoustic guitar, check out the resources and products at the website of the Stewart-MacDonald company in the USA.
StewMac Maintenance and Setup for Steel-String Acoustic Guitars Instructional DVDs
Here are some examples of the proper tools needed for professional work.
StewMac Basic Setup Kit
StewMac Nut Slotting Files
StewMac Radius Sanding Blocks and Supports