I am NOT suggesting that you shrink the databases.
The things to compare is not the list of options but the [config_value] values.
max degree of parallelism
max server memory (MB)
If it is just the 3 procs that are slower than perhaps it is worth rewriting them.
Perhaps this will perform better on the new version:
select bs.mrn, bs.accessionnumber
from tblCreateBioSpecRecords bs
left outer join tblProcessedSpecRecords ps
on ps.mrn = bs.mrn
and ps.accessionnumber = bs.accessionnumber
where ps.mrn is null
group by bs.mrn, bs.accessionnumber
Be One with the Optimizer