Yes something is definitely wrong here. Flash has described how things should be. All holes must be cleaned out of old thread. I use a hand held pin vice available off Ebay with very fine drill bits. Use small small T shaped pins (used by people who make quilts), there are lots of pictures showing these in my restoration posts.
To pin correctly and line up the holes you have to count the holes on the outside insert the pin and then flip the helmet over, look inside and count the holes on the inside. To start, I usually go 4 holes in from the tip of the visor, I line up to the fourth hole in the shell, then insert the pin half way. I want a space between visor and shell so I can count both visor holes and shell holes. Next count across 10 holes in visor, 10 in the shell and insert the pin. You should be able to repeat 3-4 times ie 3-4 pins before you have to push all pins into the shell because the visor is flopping around. Now you count holes on the outside as usual but you have to flip the helmet (liner pulled out) and count holes from the inside of the shell. I use one of those magnifier lights when I do this indoors. However, the best light is natural sunlight, you can turn the helmet so as you actually focus that light on the inside stitch line when you count. Other....hints: Before cutting the visor off to stitch, take a pencil and draw lines on the shell across the hole. This will give you a series of marks along shell and visor to help line things up. Second, there are always lines in the finish made by the rear spine both on visor and shell. You can line these up and actually start pinning from the middle of the visor. Third, and specific to the rear visor, the tips of the visor are stitched with a loop of thread so there is one hole, the very first one which is below the rest of the stitch line and close to the shell rim. This is where you start, push your needle up through this hole from inside, then into the second hole which is actually in the stitch line. Do this twice creating a loop of thread and then start stitching across. Fourth....breaking thread...you must use beeswax to coat the thread and you must do this multiple times as you go across the visor. Also you must move your needle (change position) along the thread as you stitch. Stitching (friction) causes wear in the thread where the needle is located. If you don't shift the needle, it wears through and breaks.
Regarding thread, the most easily found and the closest to original thread is the linen book binding type. You can buy it online in various thicknesses. You can not buy thread today of proper thickness that does not have man made fibres in it which will "light up". I use vintage cotton thread from the 1940's and 50's when you could still buy thick cotton thread. You can still buy 100% cotton thread today but it is too thin and only suitable for stitching cloth. You can use it for officer liners. Good luck.