If you are no longer in a bona fide marital relationship at the time of filing for the removal of conditions, you cannot file it jointly and you really cannot file it by yourself if you are still legally married.  However, if you believe that your marriage is reconcilable and you think you will reconcile, I'd probably suggest that you wait until the last possible  moment to file the I-751 and, hopefully, you would be able to file it at that time together with your spouse.  If you say you can't file the I-751 for another 3 months and the I-751 can be file within 90 days of the expiration date, that suggests that you might have about 6 months before you have to file.  If that's the case and you feel that this marriage has a chance, perhaps 6 months will be enough time for you two to determine that.