When winding my secondary coil I accidentally overlapped a couple wires (~10 out of 900). I know that you can't overlap wires because the voltage drops but is overlapping just a few wires okay?
Overlapping the turns causes several problems.
It increases the voltage stress across the wire insulation by putting a turn next to a wire not one turn away, but several turns away. This will cause premature failure on the insulation, especially as you push the secondary to higher voltages.
It makes the profile of the secondary surface uneven. This can provide a break-out point for discharges that can damage the insulation, and sap the energy of the secondary preventing buildup to the maximum voltage that your topload can stand.
Still build the coil. You will learn valuable lessons from building and tuning the whole thing, even with a sub-standard secondary.
Once you have the whole coil working, then invest some time building a uniform secondary. First of all, diagnose why you failed to make a good secondary, then solve that problem. This may mean building a winding lathe rather than hand-winding, taking more time hand winding, equipping your winding lathe with an automatic feed, or merely arranging your feed spool of wire so that the wire comes out steadily under a small but constant tension.