Motor is still in the bike, front cylinder looks easy (about to start on that) rear cylinder looks a little harder. I would appreciate any tricks. Not sure about heads yet, if you think there is some power to be had on top of milling the cylinders I probably will.
I expect the cam timing to be off after this, hopefully there is a good cam timing option without having to buy adjustable gears.
There is definitely more power in milling the heads and still can run pump gas too. It is all in where you want to be compression wise and don't worry, there should be near 0 reliability implications if performed correctly.
Here is a brief procedure/description of the rear cylinder head removal with the engine in the bike.
Remove the rear exhaust stub pipe. Everyone says the rear header pipe is a pain to get off. I think it is pretty easy actually. From the left side of the bike the left bolt can be easily removed with an allen socket and an extension or two. The right side one is trickier, but with a few extensions again and a U joint it is pretty easy, if you remove the right foot peg hanger and tie it up out of the way.
After the rear cams are out and the cam chain tensioner has been removed, the intermediate/idler gear bolt needs to be removed. This is the tricky part.
You will need a 30mm straight section of a 10mm allen wrench or press out the bit section of a 10mm allen socket. It can be a bit shorter, but not much longer.
Place the allen wrench section into two 10mm box end wrenches. I use two wrenches for extra grip on the allen bit, slide it between the frame and the engine and twist it into place so that the allen is fully inserted into the bolt. Now you might be able to just muscle it, but usually on an engine that has never been cracked apart, it might take a couple of smacks with a dead blow hammer, or a short cheater bar to crack that bolt loose. It will pop loose. From here thread the bolt out as far as you can. Now try to wiggle the bolt out carefully. I have gotten some out easy and some are a pain. If it does not come out the next secret is to use the thrust adjuster that seats on the cylinder head right near where you are working. Take the engine mount bolt out and loosen the lock ring with the Suzuki special tool. Back the ring out or take it off. Use a 19mm 6 point socket and crank the thrust adjuster in farther a mm or two. This will flex the frame out slightly. You should now be able to get the bolt out, drop the gear down, get the chain off and get the gear out. The rest is easy.
I do this all the time, so It can be done.