I do not know what is the scale of your data, but something like calculating edit-distance might help you.

from Bio import SeqIO
import editdistance,sys

fa1 = SeqIO.parse("1.fa", "fasta")
fa2 = SeqIO.parse("2.fa", "fasta")

for rec1,rec2 in zip(fa1,fa2):

    if ( rec1.id != rec2.id ):
        print "The sequences are not in order. Exiting"
        sys.exit()

    length=len(rec1.seq)
    dist=editdistance.eval(rec1.seq,rec2.seq)
    print rec1.id,100-((dist*100)/length)

output:

trinity5_comp_3_0_1 100
trinity5_comp_9735_1_5 80
trinity5_comp_645_0_2 90
trinity5_comp_3169_0_1 100

Assumes the sequences are in same order always. If your fasta sequences are very long, this is definitely not a good solution.

If you want to run cd-hit-est-2d on each pair of sequences:

Make a backup of your files.

cp 1.fa 1.fa.bkp
cp 2.fa 2.fa.bkp

Add a prefix to your fasta header. Check how it works for your system.

sed -i '' -e '/^>/s/$/.1/g' 1.fa
sed -i '' -e '/^>/s/$/.2/g' 2.fa

Then split the fasta file into individual sequences.

for fa in {1,2}.fa
do
curl https://raw.githubusercontent.com/gouthamatla/fasta_File_Manipulation/master/SplitFastaFile.py | python - ${fa}
done

Now you have all your sequences split with .1.fasta and .2.fasta suffix.

Then run cd-hit-est-2d in pairwise manner:

for sample in *.1.fasta 
do
base=`basename  ".1.fasta"`
echo "cd-hit-command $base.1.fasta $base.2.fasta" | parallel --jobs 4
done
rm *.1.fasta *.2.fasta

change the --jobs according to available cores.