Man I hate to hear about these type of things. Can't begin to imagine what a nightmare it is.
Now, A few thoughts that may be varying degrees of useless to you:
1) if you make it out to the other side of this and start again with a new contractor: in addition to paying progress payments/draws you would likely be better protected by issuing payment via joint checking or requiring the contractor to provide partial lien releases from all material/labor suppliers
Also, have the bank hold back 5% minimum ( preferably 10%) of each draw in a retain age account to be paid ~90 days after completion upon receipt of final lien releases from all labor and material suppliers.
2) for your current lien situation you could explore the option to bond around the liens
3) if you were planning on living here for the extended future (not selling anytime soon) you may only have to worry about the liens creating issues with future financing or generating interest from the replacement contractor/trades
Best of luck. Hope this all resolves for you.
Thanks & Gig 'Em