Id say to just get a new auto-siphon. I've had to replace mine when I started getting infected yeast washing and took a good hard look at all the cracks in my auto and just decided that it Wasn't worth it. I still use the thing for moving secondary into my kegs (after its siphoned out a whole carboy filled with cleaning water and is washed out) , and use a stainless steel racking cane to extract beer from primary so my washed yeast will be safe.
for the price of replacing the auto (which are cheap), its just a better decision than loosing an entire batch of beer to infection (or in my case, loosing yeast washing's).
Id also suggest using a bit less than recommended for priming sugar, just to be safe. The beer will get carbonated up over time anyway, and its best to play it safe. But then again, difficulty with priming bottles DID eventually push me into kegging :P
best of luck!