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Again, I believe you're right - I'm just having a problem getting it to release its decades-old grip on it. So far, I've tried heat and PB Blaster, a rubber mallet, harsh language, gentle prying, the aforementioned use of a crowbar...I'll Get it, I just don't know how yet. And the pistons are of course stuck in the cylinders, and those pistons are of course stuck at the bottom of their travel; so that makes it even more fun!

Once you release the head and barrels from any retaining bolts, if the crank will rotate then it may lift the
barrels off the top case and raise the setup on the cylinder studs??? This would give you access from the top and bottom of the assembly.
Heat and Deep Creep are your friends here. I have heard of a steering wheel puller being used to separate the barrels from the pistons. Just not familiar with how that tool works.

"if the crank will rotate then it may lift the barrels off the top case and raise the setup on the cylinder studs??? This would give you access from the top and bottom of the assembly."

Right - that's what I was trying to find the M10x1.25 threaded rod for in another post - I was going to take out the head mounting rods and re-insert the threaded rod with some nuts on it, and use that to put a wrench on it and 'jack up' the head off the piston...I may try Chainman's method, but I'm not sure where and how he means to use it as a fulcrum without marring the head mating surface. I may try a regular crowbar underneath the fins, somehow, but I hate doing that. I'll try to get some pics up here today.

As is, the head is loose, but I only have about a sixteenth of an inch between the block and the head. Currently the bike is stuck in gear, and the gear shift won't shift; I was thinking about putting the chain on and trying to rock the bike back and forth in the hopes that the penetrating oil I've put in there will do some good but haven't tried that yet. This bike is locked up good!

But first things first, I want to get the sprocket cover off so I can get to yet Another screw that I can see underneath it that is holding on the left-front side cover - there's Always One, y'know?

Okay, so I was able to spend a little time in the lab working on the 400, and I think I know what the problem is - but I may be wrong....

As was pointed out that the problem may be rusted-in locator dowels, I don't believe it is; I think it's the big seal in the middle of this other sprocket cover, as seen here - but again, this is NOT the sprocket cover I'm working on:
KZ400 Sprocket Cover by Dr. Frankenstein1, on Flickr

I think this because after applying more heat, PB and judicious use of a crowbar, I managed to break off a piece of the cover as seen here, which of course caused several colorful comments from me, but is fixable. It also opened it up enough for me to see where the screw goes into the cover, and it's IN THERE where the dowel is, at about the 11:00 o'clock position above that rounded piece on the frame; but the dowel is loose, I can see the little seam expanding a bit when I pry on it;
DSCN2190 by Dr. Frankenstein1, on Flickr

However, as I pry on it, it feels like it's stuck right in the middle of the cover, and indeed I can see that big round seal going kind of cock-eyed on its shaft - I don't have a picture of that, which is why I attached the pic of the cover above, but That is where I think the problem is; but it does not want to budge. I've hit it with PB Blaster and I'm going to try to get some heat on it, but I'm open to comments/advice. This cover is a true PITA.

Oh, yeah - FYI, here's all the room I have to move the head. The pistons are at the bottom of their stroke, which makes it More fun! (This one's a little blurry...)
DSCN2191 by Dr. Frankenstein1, on Flickr
DSCN2192 by Dr. Frankenstein1, on Flickr

If those methods don't work for you here is a design that may work like a puller off the existing cylinder studs and will press down against the pistons in the bores. Not too expensive for the parts and any threaded rod of your liking and length will work with SAE fasteners and nuts etc.

Dr. Frankenstein wrote: ↑Wed Feb 23, 2022 9:58 am I may try Chainman's method, but I'm not sure where and how he means to use it as a fulcrum without marring the head mating surface.

i only released the cylinder from its gasket. sorry for any confusion.

I once unstuck a rusted 305 Honda piston just by beating on it with a block of wood on the piston. Then, of course, I needed a new liner because it had broken the top flange off and moved the liner down in the barrel...

A mechanic that I enjoy on Youtube (Watch Wes Work) is located in the upper Midwest. Gets a lot of salt corroded vehicles with frozen fasteners. Things he uses include air-powered impact hammers that give continuous shock that eventually breaks the corrosion's bond.

Dr. Frankenstein wrote: ↑Wed Feb 23, 2022 8:54 am Again, I believe you're right - I'm just having a problem getting it to release its decades-old grip on it. So far, I've tried heat and PB Blaster, a rubber mallet, harsh language, gentle prying, the aforementioned use of a crowbar...I'll Get it, I just don't know how yet. And the pistons are of course stuck in the cylinders, and those pistons are of course stuck at the bottom of their travel; so that makes it even more fun!

What did the oil you drained out of the engine look like?

Stygian Black:
DSCN2218 by Dr. Frankenstein1, on Flickr

Here's another pic with a flash - a deep gunmetal gray...
DSCN2219 by Dr. Frankenstein1, on Flickr

It smelled a bit burned, too - any clues?

No clues.
Stygian black and gunmetal gray sounds hauntingly ominous though

Did you get the side cover and barrels off the engine?

Not yet; I've been dealing with some other things and haven't had much time in the garage. I like the plans though; I'll be giving those a try as soon as I can. The side cover meanwhile continues to give me the finger. I will report as soon as I make some progress.

If you use those plans I think I have the nuts on the cylinder studs backwards. You would need them on the top of the studs, since the threaded rod when tightened will push upward. In that design it would just lift the board off the studs. Reversing them on the top will give the needed downforce to hopefully push down on the pistons.