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Not really, I don't know much about it myself. I've seen people recommend VisualVM for this sort of thing, you may also be able to use Minecraft's Profiler class. If you enable profiling in Minecraft (/debug start), you may be able to add a shutdown hook (Runtime#addShutdownHook) that saves the profiling output to a file (e.g. by running /debug stop). This would allow you to see what took so long after the server is stopped by the watchdog.

Probably because the item is still being given to the inventory as 0/4/8/12 but you registered an item renderer for a different metadata value. i.e. this chunk: @SideOnly(Side.CLIENT) public void getSubBlocks(Item itemIn, CreativeTabs tab, List<ItemStack> list) { // item , amount, meta list.add(new ItemStack(itemIn)); list.add(new ItemStack(itemIn, 1, 4)); list.add(new ItemStack(itemIn, 1, 8)); list.add(new ItemStack(itemIn, 1, 12)); } If you're going to change your metadata values in one place, you need to change them in the other. THIS IS IMPORTANT, IT IS NOT ARBITRARY. Most importantly, you need to use the metadata values that your block actually drops when broken. If it exists in your inventory, then you have an item. item = new ItemMultiTexture(tudorSet, tudorSet, ModBlockTudorSet.subTypes; Surprise, there it is. In order to override the unlocalized name you need a custom ItemBlock class. Surprise! Alternatively, pass a name function to the ItemMultiTexture's constructor. E.g. here is how vanilla handles the stone variants: registerItemBlock(Blocks.STONE, (new ItemMultiTexture(Blocks.STONE, Blocks.STONE, new Function<ItemStack, String>() { @Nullable public String apply(@Nullable ItemStack p_apply_1_) { return BlockStone.EnumType.byMetadata(p_apply_1_.getMetadata()).getUnlocalizedName(); } })).setUnlocalizedName("stone"));

There's a list of tutorials here. Some of them have been updated to 1.11.x, some of them are only on 1.9.x/1.10.x but the versions are fairly similar.

Then the issue is probably with another one of your mods. Try removing all of the Malisis mods, I seem to remember them messing with Forge's internals at some point. If that doesn't fix it, post the complete FML log (logs/fml-client-latest.log); it may contain some useful information about the issue. If it doesn't, you'll need to remove mods until the issue no longer occurs.

Try setting the opacity as white, but at 1% opaque. When rendering transparency as transparent, Minecraft ignores transparency values below about 10%.

Technically, Minecraft does not stand for that. It simply renders what it was given. The PNG format makes use of something called "Transparent colour". Most image-editing software that exports into PNG will have a "Transparent Colour" option when exporting. Would you mind if I asked what software you used? I haven't seen a non-white default TC outside Krita, so far.