For the assemblie use, Flye it seems like is the best tool for plasmids:
flye --nano-raw your_long_reads.fastq --out-dir out_nano.fasta --threads 4
Your can corrected the
--threads parameter to match your computer resources.
As for the counting of the tandem repeats because you have both references
I have the sequences of the plasmid and the insert.
I think you can merge they in a single reference fasta file (plas+repeats+mids) with a text editor tool or a script (if you need help with this please provide a sample dataset and a desired result).
When you have a reference you can map your assemblie to it with an aligner of your choice. For example with MUMMER (dnadiff):
dnadiff -p my_output your_builted_reference.fasta out_nano.fasta
Check the output.report to see the statistcs of the alignment. Ideally you need to see an "AvgIdentity" of 100.00 but because of natural mutations and some errors noises in the nanopore reads it is probable that you assemble has some SNPs or other minor alterations so check the overall structure. For some visualization try this site to see your output.delta file click in "iteractive dot plot" you need to see a straight diagonal line in the plot (like this).
I think this will do.