Very precarious situation there. Sounds like you are cross-threading. Normally I'd say chase the threads with a tap and try again, but having any metal flakes in there from that would be bad, especially with removing the filter.
Inspect the banjo bolt to make sure the threads are in good shape. If they are questionable, either run them through a thread die or get a new bolt.
Slowly reinstall the bolt by hand, make sure it is going in straight. Avoid using a wrench to force it further.
If it's binding still, then consider these two options:
1. Run a thread tap in there to clean up the threads. This will make it so you can get the bolt in smoothly, but try to clean out any metal shavings generated as best you can, maybe by using q-tips.
2. Gently (seriously, don't force it) wrench it in. Make absolutely sure you are straight when doing this. If you can't get it to go then you have to go to step one.
Lastly, when you are installing it, start by applying pressure to the bolt and turning it counter-clockwise until you feel it click into place. This means that the start of the threads for the bolt and hole have aligned and should minimize the chance of cross-threading.
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