Congrats on the new toy.
I frequently fish East Bay in my PA14, targeting salmon, Lakers, cisco or whitefish and occasionally perch. I'm not a bass guy, but suspect that you will be doing cast/retrieve for them. If so, then consider jigging (rather than trolling) for the lake trout. That would totally alleviate the need for "troll-worthy" rod holders and open up the possibility of just using the corner holders on an H-Crate for transporting your rods. Personally, I prefer vertical rod storage to horizontal anyway, since it gives you more cockpit space when dealing with hooked fish, nets, etc.
I do a lot of trolling for lake trout, salmon, steelhead, etc using the Hobie H-rail rod holders. But these are definitely not quick to remove for placement of your cover. The knurled red cam lock knob that fastens the holder to the H-rail always seems to end up jammed tightly against the gunwale, making it a PITA to release the cam mechanism for adjustment or removal. And unless you want to spend most of your budget on gear to get a lure 80-150ft down where the Lakers feed, jigging is a far simpler and very productive way to go out in GTB. Although I routinely troll elsewhere with one downrigger line and one lead core line, I try to avoid that in East Bay where there are such rapid and dramatic changes in depth / bottom structure. The majority of my lake trout from there have been caught with a simple 2oz untipped vertical jig.
Good luck out there - it's a great fishery!
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