I spent the last two weeks pimping my ride so I'll throw my $.02 in.
For flush mount rod holders, I prefer the ones from KFS (KayakFishingSTuff) which are $7 a piece but have a cap on the end to keep water from getting into the hull of the kayak. I think the ones at BPS/West Marine/Boaters World/etc. are intended for boats and have open ends that lets water drain through them.
On my kayak, i have 2 angled flush mount rod holders for trolling spinning rods and 2 Scotty Flyrod Holders for carrying 2 fly rods. I also have one Ram Rod Holder mounted up front that can hold whatever rod I'm using at the time (fly or spin) and can swing out of the way if necessary.
As for fishfinders, no need for a portable one. You can use any fishfinder you want and power it with one of a few choices. You can use a rechargeable 12volt sealed lead acid battery or you can rig up a rechargeable AA box with 8 batteries thats smaller and lighter. The SLA battery will get you 20-30 hours of use, the 8 AA's about 10 (I think). The AA's are smaller and lighter, the 12volt is big and heavy. Some people have also powered there setup with cordless drill batteries, RC card batteries, etc.
There are a few articles on KFS regarding power setups you shouuld check out. And I'd recommend buying as much as you can from KFS: No sales tax, and ground shipping from NJ takes 1 day (essentially overnight). I still had to get some things locally from West Marine/Boaters World/BPS/and Dick's but the majority of my stuff came from them.
Oh, if you're going to add an anchor trolley or other non-stretch lines, go to EMS in Annapolis and buy their black 4mm rope that has a reflective thread run through it. Its cheaper there than anywhere else I've seen it. Its in their rock climbing section.
I'll try to get a pic of my kayak posted as well. Also, if you want assistance doing it I'd be happy to help. I live in Columbia.