I did this recently & had planned to use the router ... did, in fact, except in the places you described where it wasn't manageable (would have been possible with a jig, maybe, and/or a longer bit designed for such things). I ended up finishing with a sabre saw (same deal with the sink cutout). The formica chipped in one spot, I think because I was pushing the saw rather than letting it cut.
Anyhow, I got a nice clean edge that didn't need much fixing before gluing the end cap on. Most of my sabre-sawing was on the back, but when I did it on the front I protected the countertop with masking tape.
You can put tape on the saw instead, but in my experience it wears through more quickly.
I'm no expert, having replaced only one countertop in my life. It came out okay. If I had paid a professional, I would have expected (and certainly gotten) better results ... but I wouldn't have had as much fun OR been able to convince my wife I needed more tools.