I have currently 2 Primary Complaints for the current state of the mod, the first and more important one is that currently the mod spams very quickly the whole console with error messages while the player is either resolving the issue or doing something that makes the mod think its broken.
personally i think instead of a timer its better to measure how many messages have been written in chat since the last time it showed the error, as to make sure the message should be for most people only visible once or twice at the same time.
as a side note, any mod like for example "Blueprint Sandboxes" which im using to plan complex designs or any other mod which teleports the player to another surface or provides such an ability if multiple surfaces exist it will cause the mod to think its gone despite being in the inventory of an entity. the most obvious solution would be to first check every entity on the current surface and then every entity on every other surface if its in there inventory which should catch many instance of the cube being somewhere else but there is probably a better way to check all entities with inventory and priotize in which order to search them. also if the cube is on another surface its probably better to warn the player that they are leaving the cube behind rather then warning that its gone missing.
Second and less Important Complaint is made up of 2 Smaller issues feeding in to 1 Complaint, firstly in instances such as steam Power Production the Amount of water consumed by 1 boiler at 100% usage is higher then pipes can move through all connections at the same time, same goes for the steam output which is also higher then the total amount pipes can move through all connections.
so even the best possible optimized setup would still mean at a too high usage will slowly drain the setup and thus lead to a slow brown out because its reporting a higher capability then what it can actually do.
the second issue is and i realize this should come after that stage of the progression is content complete but the ratios dont allow for any design that is satisfyingly optimizable, which means there is always at minimum 1 step in the process thats not 100% efficient even if im using a mod that makes the pipes capable of moving the required amounts of steam and water.

oh, also there is some compatibility issue with mentioned "Blueprint Sandboxes" mod which prevents it from propperly switching the player between the seperate player character used in the sandbox, all the configuration differences etc. normally it would give me my hotbar back setup the same way it was when entering the sandbox but with ultracube it doesnt do that and i keep everything when transitioning between sandbox and non sandbox surfaces.
its possible that there are also more things not working as intended as well but thats the only thing i have noticed so far going wrong.

Thanks for noting the problem with Blueprint Sandboxes. These sorts of mods aren't properly supported yet, but I plan to do a pass and see what I can do to fix them at some point.

I pump water anf steam through the boiler at the max rate of 12k/s. No modded pipes. Storage tanks are vanilla pipes with larger capacity. Either alternate between pumps and storage tanks or just pumps for straight sections and tanks for corners, for the high throughput sections. I find the puzzle of not having bottlenecks different from vanilla so I'm enjoying it.

But later in the game you will be able to have multiple boilers with fuel made from liquids or by using phantom ultradense constituents.