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Yes, the LLC can withdraw as a party.
You may need to get the opposing party's agreement to dismiss these claims, but the other side should agree to it (if they refuse you will need to file a motion with the court asking to dismiss the LLC as a party - the court will almost certainly grant it, and the other party's objection to a stipulation will only have wasted everyone's time, including the court's and they will look very foolish (particularly if you put your request to stipulate in writing, and attach it as an exhibit to your motion).
You and your ex-wife will need to represent yourselves "pro se" (you cannot represent one another), but you do not need to change the format of your complaint, etc. Just make sure that all of your moving papers, responses to discovery, etc. are coming from each of you (you can each sign the same documents if you like (or if appropriate), or you can sign and submit individual documents (if you like, or if appropriate)).
Yes, start with the letter asking them to stipulate to the motion (you can even send them a draft copy of the motion (this should be a simple, one page, motion to withdraw the LLC entity as a party).
You do need to make the motion to withdraw the LLC, even though it is no longer a valid entity, the court does not automatically end the suit as to that entity (remember, most suits create potential liability for both parties, even if it is only a potential claim for court costs (filing fees, etc., usually minimal), so it will take a court order at this point).