I am getting ready to install a Ram Mounts rod holder in the stern of my canoe. My questions are:

Do most people troll with the rod on the opposite side they paddle?

How far forward and high is the ideal position for the reel?

In the photo, you can see what I am thinking. I paddle left so rod on right about 6-8" above the gunwale, but I can mount it about anywhere. It also "seems" like I can even mount it on the paddling side without it interfering with paddling much, but maybe this is a bad idea. Thoughts?

I think your thinking is solid. I have my rod holder mounted to the left side as I tend to paddle more on the right, but I do switch sides paddling while trolling without issue. I just need to be mindful of my rod while doing so.

I don't think there is a universal best position for your rod holder. Just be sure you can reach it quickly, but give yourself some distance so it is not in the way constantly. This will depend on your height and arm length I suppose.

I have found, especially fishing in Quetico with barbless hooks, it helps to have your paddling partner continue to paddle a couple strokes until you have the rod in your hand and are in control of fighting the fish. You want to keep the rod bent with tension on the line the whole time.

"You want to keep the rod bent with tension on the line the whole time."
I don't reach for my rod until the rod is fully loaded after I paddle a few times. This is especially important when your rod holder is in front of you and when paddling into the wind.

I've got two rod holders on the canoe. One in front and back. I mounted the one in back on the right side because I already had a fish finder mount on the left side. In the front of the canoe I mounted the rod holder on the left side. Both of us can paddle on either side while trolling and it doesn't get in the way. How you position the upper portion of the rod holder will give you more room for paddling as well. Most rod holders are very adjustable for that and you'll find how you like it while out fishing.

This won't help the OP as he has wooden thwarts, but perhaps someone will find it useful. My canoe(Souris River) has 1" diameter aluminum thwarts and this is where I have my rod holder mounted. I use two U-bolts with a short piece of vinyl tubing to act as a cushion between the thwart and the bolts. I have the bolts tightened down so there is no lateral movement, but I can still rotate the whole mount forward and out of the way when not in use.










Pushed forward, while jigging for walleye.










Unlike the stern of the canoe, there is no great place to mount a rod holder within easy reach. Here is my solution for a front rod holder. It consists of just a simple scrap of plywood with bolt clamps to secure to the gunnels. My son typically sits in front and he has a piece of pool noodle attached which he sometimes hangs lures on temporarily.










It may be simple, but it works.

which side ? opposite your power side , but everybody needs to switch eventually , give your rod holder enough room forward for when you do need to switch sides paddling . angle for me depends on whats on the end of my line , deep divers i like the rod to be up a bit , spoons/sinkers more level , (never tied snaps weights, cant comment)

I dunno if this helps or not but here is my setup on my NW Solo.. The problem is getting them out of the way of your paddle and still close enough to use.. after many many trips this is what I ended up with as far as the setup goes for soloing.. my tandem setup is pretty much the same but only one rod.