First and foremost if you ask why i did this, i will respond with "Because Fun".
Second, each machine would have a "Offline mode", Tinkering with Online machines its a stupid concept with dire consecuences (Electrocution or Unexpecte Explosions) :D, wires should also be removed before doing any modification.
And third so far i have 2 types of system (I was going to make a 3 but it was too much for what minecraft can handle >.>, Even though the second system could also be a little too much):
Module Upgrade System (V1.0): A Tier Based System. Each machine possess a total of 12(9 with the tiered machine) slots for modification but only the first one its available. System its valid as long as the number of upgrades its 3 or so (Optional). To increase the number of available slots i deviced 2 ways for it, Either a Tiered machine block (I.E Macerator Mk1, mk2, etc) giving 3 spaces per tier (3/6/9) or a Motherboard system in which only the first slot its available on the machine, in this slot you would place the "Motherboard Upgrade Mk1/Mk2/Mk3" granting you access to the next 4/4/3 Slots in your machine. In this tiered system Mk2 and Mk3 upgrades wont work without the preceding upgrade. Number wise i dont have idea since i suck at math :P.
If the machine is in offline mode the Upgrade grid GUI will show up instead of the Process GUI (I suck at paint too so dont mock me D: ) :
Module Upgrade System (v2.0)-Link System: A more ambitious system that the v1, it kinda works similar on how a Nuclear reactor (Minus the checking status every tick and really big explosions), the idea is that it only checks the circuitery when a machine goes from off to on or when chunk/world its reloaded. In case of explosion, it would limited to the machine block itself and a chance to lose some of the components inside. This system would be based on reaching a certain "Equilibrium" with some parameters:
-Energy Reserve (How much Energy the machine can hold internally)
-Energy Comsumption (How much Energy the machine use to realize a task)
-Efficiency (How Fast the machine realize the task)
-Maximum Voltage (How much Eu/t the machine can receive)
Each Module Upgrade will have a special value (I call it weight for now, couldnt come with a better name), each Machine/Motherboard tier can only hold a maximum amount of total weight before it collapses when the machine gets turned on (Kinda like Heat in a nuclear reactor, too much heat is baddddd). If the total weight exceeds what the Motherboard/Machine Tier can hold its behaviour will be affected, Worst case scenario its that the machine could end up exploding, other effects would be a performance it or more weird things. Like the MUS v1 system, this one would use either a Machine Tier (Mk1,Mk2,Mk3) or a Machine with a Single Special Slot to introduce the motherboard (Mk1,Mk2,Mk3), the tier would indicate the amount of slots you will have available and how much weight the machine can support before collapsing.
Modules would come in 4 types and 3 versions each, each type of module would increase 1 Stat slightly but in turn it would decrease 1/2/3 stats by a lesser amount. MK1 versions can be placed anywhere, MK2 version can only be placed nearby MK1 or MK3 Versions, and MK3 versions can only be placed nearby other MK2 versions. If a mk2 version its placed near another mk2 version there will be a performance hit in the form of a penalty weight. Also each version will only affect their own type, Mk2 Efficiency module will not affect MK1 Energy Reserve module and there will be a Weight penalty because the mk2 isnt near a same type of mk1/mk3 version also same types of modules will Link themselves and transmit every upgrade they recieve from the MK2/MK3 versions (I dubbed this as the Link System). MK1 modules would have a static increase in their numbers, Mk2 would increase the stats of linked mk1 by a certain % (Both the Extra stat and the penalty to other stats) and Mk3 would decrease the penalty incurred to other stats (Static or % havent decided yet) of linked mk1/mk2.
There could also be a 5 type of modules with a high "Weight" parameter only that would give the machine special traits like a % chance to get extra items (Limits apply), More Input/Output Space, A "Heat" system similar to the induction furnace for the other machines, etc.
Well that was fun, let me know whats your opinion on this, Devs Feedback its very appreciated so i can learn about the limitations on the minecraft system so the next time i could design even more realistic systems.