I don't claim to know the exact numbers for this sort of thing, but I've read that scripted intersurface item interfaces that work every tick - exactly like these Underground Shafts - make quite a hit on the performance in the long run. As this mod is in its very early stages and there aren't any factory designs yet that would be broken by a significant redesign, I'd like to propose a different way to transfer items (and possibly entities) between the levels, one that would minimize the amount of scripted calls.
Of course, the most obvious way to transfer items between levels is by manually bringing them along in a player's inventory - works great as is, only mentioning it for the sake of completion.
Then, I suggest removing storage space from the manually climbable shaft, dedicating it instead as an entry/exit point for the player, and adding a specialized Cargo Elevator shaft. It follows the same placement rules, but does not allow a player to traverse it (there is a tight, cramped elevator inside instead of a ladder) and has a bit of storage space equivalent to, say, a steel chest. However, this inventory is only available at one end of the shaft at a time - while the elevator's doors are closed on a level, it can neither accept nor take items there. The elevator can be set to move between levels on the conditions of Full Cargo, Empty Cargo, Time Passed, Inactivity, Item Count and Circuit Condition - like a simplified train, if a train only had two fixed stations and couldn't carry passengers nor fluids - as well as called or sent away manually with a button.
There is a delay before the elevator arrives after it has been sent - around 15 seconds or so - and a moderately minor power draw during the movement. This adds to immersion and provides a minor logistic challenge, but most importantly aids with performance by encouraging players to move resources in singular batches instead of a constant trickle eating at performance at every tick.
As a possibility, further research may unlock larger elevators - say, 3x3, with 9 times as much space and 5 times as much power draw. Look up "Warehousing Mod" for inspiration.
And later, players can research the ability to construct large, multitiled elevators that move entire sections of the floor at a time (two controller/engines adjancent to a special flooring on both ends - multiple elevator floorings forming a rectangle will move together - with a separate tiny buffer surface to serve as a transition during the movement), with all the buildings and entities on it, including the player. These Industrial elevators allow for a great amount of applications such as moving liquids (in storage tanks), trains on tracks, large warehouses and other storages, machines... and more! To compensate, they have a large power load and a considerable movement delay. Industrial elevators cannot move if the boundary of the floor rectangle is crossed by a multitiled building, has an unbroken pipe connection (use a pump) or includes an underground belt/pipe section, as well as there is a building on the other end.
If you like the sound of it, please let me know if you want to brainstorm the details together!)