Yes, the professional Eavestrough installers make it to length right on site - theres a big roll of flat aluminum in their truck, and it goes thru a mold or press, shaping into the eavestrough profile you've picked, and they make it to the right length, so the only joints are at corners (or if they have to slope it both ways away from the centre of the run). I think when friends had their whole house done last year it was somewhere around $5,000, a large house with lots of roof area so they had to go oversized for the eavestrough and downspouts.
But you should have that done after you've done what ever you want with the roof itself. Is the roof structurally sound? thats the 1st consideration. if you're gettting Ice dams theres likely not enough insulation in your attic, or enough ventilation in the attic so that the outside roof is getting warm and then cold. does your current roof have like 4 or 5 of those square vents near the ridgeline, and do you have vented soffits under your eaves? Thats often a problem that causes the ice dams. I'm not sure about adding the wooden strips that the metal roof parts attach to overtop of lots of layers of shingles, which sounds like you might have if the roof is looking kinda "wavey". I and a friend and his neighbour (a contractor) did his metal roof - we went over the existing shingles, he had 2 layers, and had been getting ice dams on the lower-sloped roof. After the metal roof went on, they didn't have the ice dam problem anymore.