C.R. LAURENCE 877 CRL Super Spacer Sealant is really good stuff, they use it to hold windshields in to cars. The problem is if you use it here and have to do a window repair in the future you will not be able to take it apart. Remember they cut windshields out of cars. I would take the window out to do the repair. Any glass shop should provide the correct replacement seal.
If you decide to use the CLR sealant soak the tube in hot water to 30 minutes before you apply it. This will soften it and it will flow better. Also get a really good caulking gun, the cheap ones will fold under the pressure required to get the sealant out.