I was looking on Google earth and I see that it all connects through Elk Lake and Lake Skegemog and also the Torch river I believe. However, I'm not sure if you can run a boat through all these rivers and lakes due to bridges and shallow water, etc. If you can, how big of a boat could you get through? I have a 400ss and was just curious as I will be taking a trip up here early next summer.

I believe there is a dam in the way. Heard there was a dam up that way that had a crane to lift boats over but not sure if that was the one.

No

No but you can go to nearby Lake Charlevoix.

Yes, & a nice place 2 B off the big lake!!!!

There is a dam at Elk Rapids which prevents entry into Elk Lake and passage through Skegmog Lake and the river into Torch Lake. I'm not sure if there is lift capability available to get you around the dam.

I'd stick to Lake Michigan, Lake Charlevoix, Harbor Springs and the Traverse City Bays. Way more to see and do.Torch is somewhat limited for places to go for a drink or meal and no real town to visit.
But then I live in T.C. !
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The only thing you could do is hire a local transport company to haul out at Elk Rapids and drop you into Torch or Elk Lakes. But with 40 feet of boat you'll be pretty limited.

I agree with others, stick with Lk. Michigan and Lk. Charlevoix.

Torch lake is cool to tool around in but a 40ss you will be bored to tears. I took my 20 ft cc there and after 2 days there really wasn't much to see. It is a beautiful lake though.