There are needed corrections in most ALL of our trees - FamilySearch FamilyTree is a work in progress and continually being updated -
Here is a link that talks about merging - but merging is a complex porcess that I definitely would not do in a hurried process expecially if you are new to it.
Most all of us using Rootstech - probbaly have some dulicates - somewhere in our tree
BUT I cant think of any reason this will significantly impact (or have any impact) "relative matching" at Rootstech.
the LACK of connections - especially between you and your deceased ancestors - would be a factor in relative matching, though.
You need to either contact Support or to post ID references of some of the individuals in your branch of the tree. You appear to have tried to tidy up things yourself (by making merges, etc.) but ended up in a mess. Your actions are what users would usually be expected to carry out themselves, but you now need to get help (from here or through Support), as there is no automatic process for resolving such problems.