Should I sell my 5*s?

Don't sell them, but don't use them both on the same team, either.  My standard Versus team is a 5* Level 360 Daredevil with a pair of champed 3*s and I never have any trouble finding teams I want to fight, once I've skipped past the Rocket/Gamora/Medusa hordes anyway.  Whatever bad voodoo the MMR is supposed to work, I never run into it.

Well, given where you are in the game, I would personally lean towards selling them since I think you may enjoy PvP more but I think it depends on how much you play PvP vs. PvE (story mode).  However, here are some pros and cons to consider:

Cons (of keeping on your roster):

<They are increasing the difficulty you will be seeing in MMR for PvP in most cases based on your roster
<They are not really good 5* characters (within the 5* meta) overall - low mid to low tier in that tier
<You are still early in the 3* meta so they will probably continue to impact your PvP for a while (several months?),      at least until you get enough champed 3*, that when boosted, average around level 280/270

Pros (of keeping on your roster):

<They may help you in PvE since the match damage from 5* is superior to 3*
<They are 5* covers and as you said, difficult to come by
<Eventually they will not hurt you in MMR (as long as you don't keep putting iso into them) since you will build out      your 3* and eventually 4* roster, at that time, your boosted 3* and 4* will be of an equal or higher level, so it won't    impact your MMR

Whatever way you choose to go, I think the most important thing that you can do is not open legendary tokens and save your CP.  I know it is tempting to use them but at this time you need to fill out your 3* roster and begin to slowly add 4* covers hopefully as well.  You will probably find that heroic points(HP) are going to be the most difficult resource to come by at this point in the game due to all of the new characters you will roster and additional 4* characters you will gain covers for.

It would help too if you post the level of teams that you usually see in PvP. For example, I am seeing a lot of teams with level 250/level 230/level 180 etc.   That would inform us better of your MMR and seeing how much those 5* may be impacting it.  I think we might be able to give you better advice if we knew more data.  You could even post a sample of teams that you find in your PvP queue in a normal PvP.  I would choose one where the required character is not one of your champed 3* to provide data with and choose one where you have a champed 3*.   The reason I say that is because right now for example, She Hulk is the required character (who you have champed) for PvP and is boosted so that increases your MMR along with your 5* characters.  Since you only have a portion of the 3* characters champed, I would like to also see what it is doing when there is a 3* character that you don't have champed is the required character. There are other users who can better explain how the PvP MMR works and there are past articles on the forums that you can look into about it as well, I am not sure how up to date some of them are though.