The KT88 has a higher plate dissipation rating...I believe it is 42 watts instead of 35 watts, so you could bias it a bit hotter. Generally, people recomend to bias somewhere between 60% and 70% of the rated dissipation. What current you actually set it to depends on what the plate voltage is. Notice I said current and not voltage. If you set it to a particular negative voltage, you will never know what the actual current is, because the relationship isn't linear.....meaning they don't track each other exactly. Also, every tube is different and will have a different amount of bias current for a given voltage.
I'll use my 200S as an example. It has about 565v DC on the plates. I've added 1 ohm resistors to ground, hooked up to tip pin jacks that I added to the back panel so I can measure the actual bias current for each tube. I also added a seperate bias pot for each tube. If I set each tube to 41ma of current with the bias pot for each, then that works out to about 23.165 watts of dissipation. (565*.041=23.165) If I take the max dissipation value of the tube I am using, and multiply by 70%, then you can see I am just under 70% with the 6550, but I could still go quite a ways with the KT88. (35*.70=24.5 for 6550) (42*.70=29.4 for KT88) Each time you adjust the bias voltage with the pot, the plate voltage will change, as will the current through the tube. You can use the Sunn schematic's suggestion and just set the voltage at the grid of the power tubes to -55v, and call it good, but you don't really know how much current the tube is dissipating that way. If you have a bias probe, you can use that to find out what the actual current is, as I did with the 1 ohm resistors. Incidentally, I have a bias probe, and it was quite accurate as compared to the resistors. I just did mine this way so that I won't have to take the chassis out of the head to measure voltages. I guess I'm lazy that way!
You can also bias by ear, and set it where it sounds good....but make sure if you do it this way that you watch the tubes for at least 15 minutes in a dark room after you set it to make sure the plates aren't glowing orange or red. When you set the bias, whether by ear or by meter, or even a scope, you should always have all the controls at zero on the amp, nothing plugged in, and the output of the amp should be hooked to a resistor load, NOT a speaker. If you hook it to a speaker, your bias setting will not be accurate. If you are doing it by ear and don't have the necessary equipment, then you can use a speaker, but again, watch it for glowing plates!!
Your tube setup in yours sounds like a pretty good choice and it should sound pretty nice for bass. I've found that having the original Sunn 2x15 cabinet with the original JBL D140's is VERY important to the sound. It will work with other cabinets, but just doesn't sound as good. Hope that helps?
Greg