These are my suggestions. (I provide help at a local Family History Center and on 3 PAF forums online.)
Before any overhaul of your database, such as a merge, import, check/repair, or global search/replace, always create a new backup with a NEW name. Make sure to backup periodically to a CD/DVD, flash drive, or other removable media so that a hard disk crash doesn't lose everything.)
1. Check whether these duplicate spouses in your database are REALLY there multiple times, by using Tools menu > Preferences > Names > RIN so that the RINs (Record Identifcation Numbers) show after the names. If they have the same name but different RINs, they are considered to be different people and you need to merge them.
2. You will probably find that your merging is incomplete and there are still multiple records for the same person. On a piece of paper, you can write down the RINS for the duplicates, and use the RINS when merging them. See if the duplicate spouses and duplicate marriages disappear. They should.
3. Once you have your database cleaned-up, make it a practice to never import a gedcom DIRECTLY into your main PAF database. If you do, you will end up with unwanted duplicates - possibly creating hundreds of hours of delicate and tedious work for yourself. If you get gedcoms, import them into a newly-created temporary PAF database. Examine it carefully to see which individuals and families you want to import into your main database. Export (only) these to a new gedcom file, and use a piece of paper to write down how these people connect to those in your database. Then import your newly-created gedcom file into your main database and do the merges, and record the births or marriages needed to connect the new people to those who were already there. The extra time spent before importing will pay for itself over and over.