Here is a potential alternative for straight up waiting for the armor to finish that I threw together.
Let's say the EU cost and Wait Time requirements work just how you specified on the assembler table page. There could be an option component of this Assembler Module that for each one included in the combination, it lowers the time required to combine by 30 minutes or something. So if you add one of these to a basic combination it would become instant.
The module would be crafted in several steps:
6 2xIns. Gold cable
1 refined iron
2 Electronic Circuits
Heat dissipation unit:
4 10k coolant cells
4 Redstone dust
1 Dense copper plate
Energy Transfer Unit:
6 Glass Fiber Cable
1 Energy Crystal
These are combined into the Assembler Module in the following recipe:
2 Combination Units (represented by the electronic circuit)
2 Heat Dissipation Units (represented by the machine block)
1 Energy Transfer Unit (represented by the re-battery)
1 Advanced Circuit
1 Advanced Machine block
2 Glass Fiber Cables (or something)
Each piece could require the assembler table and a sum of EU to combine, with the units taking 10 seconds each, and the final module taking 30 seconds or something. This process of crafting and small chunks of waiting will still give the desired time and difficulty investment to balance the mod without being as boring as just waiting for it to finish.
Some alternative mechanics:
Each unit could reduce the time if used alone, based on the percieved cost of the unit, and adding them together into the module would increase the total reduced, so there is a scale of components a player can use based on their progress level.
Or, the combination could require certain pieces and still have a small wait time, rather then being optional, and these would be based on the tier of pieces being combined.
Anything but just sitting around waiting for an hour please :p