The broken pins are called chaining pins and are tricky for the home user to replace without risking damage to the needle plate as they are difficult to remove and the tiny burr used to hold them firm can easily open up and no longer grip the pin.
There are only a couple of things under the needleplate that are likely to collide with the needles.
1. Lower looper - with the needles
2. Both Loopers colliding with each other - not with the needles
3. Needle guards attached to lower looper - with the needles
4. Fixed Needle guard - with the needles
If you remove the needleplate and VERY gently turn the handwheel you should be able to see and feel where the collision is occuring and have a better idea of the issue.
I would strongly advise that you do not try to operate the machine until you are sure that the colliding components are adjusted. Broken loopers are approx $65 AUD and guards, tho' only about $20 AUD require some finesse in adjustment. Chain Pins approx $6 AUD
My recommendation is to speak with your local Janome dealer for advice and an approximate price to repair, replace or adjust as the case may be.
Your country's Janome website is certain to have a Dealer Locator page to list the nearest to you.
This is one occasion where it is sensible to call on the people who do these things routinely rather than try to DIY and make a more expensive hash of it.