If you start from Kyle of Lochalsh you can head to Shiel Bridge, up Glen Lichd and then climb into Glen Affric which is stunning.
Then, South over the hills to Glen Moriston and up through Inchnacardoch Forest to Fort Augustus.
Next is the Corrieyairack Pass to Kingussie which will leave you with the choices you stated, plus heading through Abernethy and across to Tomintoul -Glen Avon – Glen Gairn or Cullardoch.
I’ve done a lot of C2C variations over the last few years so feel free to ask about any other route choices.