Even when I have been doing electronics most of my life, it has been only a few years of manufacturing modules. A few things I knew beforehand, for example, that SMD manufacturing is more cost efficient and faster. The original Vorg and Freak filters are mostly SMD parts, with exception of the panel elements like potentiometers, jacks etc. Nowadays, it takes me 15 to 25 minutes to assemble a Freak module, which is quite good, but it can always be faster.
I design and build many modules, some of those are for studying, some for prototyping and others for personal use. I tend to use through-hole parts when the modules are analog because they are easier to build, especially when I need only one unit. When I need a microcontroller in the board, I simply make the whole thing SMD.
For my latest module, Wolv, I created a through-hole prototype. I was planning to make a total of 4 modules, one for me and the rest for my friends. However, before I made the modules for friends, I decided to ask others if they wanted one. If I was going to make 4, I could make a few extra. Ultimately, the semiconductor shortage made me nervous and I decided to rush to order parts for the modules.
After a few years of building modules I have learned a few things. I decided to make a small list of the tricks that I believe could be interesting to other persons building electronics. I have applied all of these tips to make more efficient the assembling of the Wolv modules. These tips are what I found to work the best for me and all present advantages and disadvantages. It is up to you to balance your priorities.
Cleaning
If you have build any board with through-hole components you know pretty well that the solder with rosin flux leaves a nasty residual on the board. The flux residuals are mostly harmless. However, I have noticed that they increase the cross-talk in some of my audio boards. I didn't make any measurements, but comparing a clean board against a dirty one I could hear the effect.
Initially I tried cleaning my boards with isopropyl alcohol, but that turned out to be very time consuming and I didn't get pristine result. Then I bought a flux-remover liquid (I don't remember the brand), and that worked just fine, but still, cleaning a single board took a considerable time. My next attempt was by using an ultrasonic cleaner. The good and big ultrasonic cleaners are not cheap. Before burning the money in one, I decided to try a small one from AliExpress.

The cleaner liquid that I got was something called "Safewash". In combination with the small ultrasonic cleaner it worked great. I had the boards perfectly clean with a 90 seconds program. But there is a small catch: after reading the indications of the "Safewash" liquid, it didn't seemed to me very safe. I had to handle very very carefully that liquid using protective gear. There may be other less scary cleaning liquids in the market, but I just don't know them. Since I build 5 to 10 boards every session, getting a big ultrasonic cleaner does not make much sense for me unless I plan to build any more boards in a single sit. That lead me to my next option.
After a bit or research I found that there is solder with water soluble flux. This kind of flux has the disadvantage that it must be cleaned otherwise it will corrode the board. The one I got is the AIM with water soluble flux and lead free. This solder is quite easy to work with. After soldering a board, I can use warm (filtered) water and a brush to completely remove the flux residuals.

In my modules all the components can be washed with exception of the OLED screens. So, I solder all the components, then I wash and dry the boards and lastly, using rosin flux wire, I solder the OLED screens and clean the board a bit with alcohol. I usually leave the boards to dry for one or two days before powering them, just in case.
A combination of the water soluble and rosin flux is what has worked the best for me.
Soldering
Many years ago I used to solder with a $15 soldering iron. When I tried a decent soldering station it was a night and day difference. A proper soldering station has temperature control. This makes easier to solder pads attached to ground planes. It also makes soldering faster because, as you jump from pin to pin, the temperature is maintained. If you use a soldering iron without a decent temperature control, you may find that you need to use a higher temperature and this will burn the flux faster making the solder tin less malleable.

One of my first investments was in a proper soldering station. A friend of mine recommended me an Ersa i-CON1. It is a very nice soldering station and I got a small range of soldering tips. Depending on the job, I use a different tip. My two favorites for through-hole soldering are a conical (3mm) and the blade tip. Both tips can hold a (relatively) large amount of soldering. If you are fast, you can carry around a blob of hot solder and go through many joints. The disadvantage of these tips is that you may waste more solder since, after a few seconds, the soldering iron burns all the flux and you have to clean the tip.

Here is a short video where I show how I solder a board using the blade tip. Once I'm done with the first pass, I make a second round just fixing the small issues and verifying that all the points are correctly soldered.
You may have noticed that when soldering, I have all the components trimmed and in place. We are going to cover that next.
Holding the components
Often times, when building a board I follow the convention of placing and soldering the components according to their height: first resistors and diodes, then ICs, ceramic capacitors and the rest. Having long terminals makes easy to flip the board without dropping the components. However, the long leads make a bit harder to solder the components since some of the terminals may get in the way.
I have been an enthusiast of 3D printers since the RepRap times. The most common use of my 3D printer is to make tools to improve my workflow and printing toys for my children. One of the earlier things I printed was a lead bending guide like this:

That tool is nice, but it has the disadvantage that you have to bend the resistors one by one. To solve this, I created my own version that has two purposes, trimming and bending the leads of 10 components at the same time.

I know that there are commercial tools to do this job, but since I'm not building thousands of modules, my 3D printed tool works just fine. It is not perfect, but it is good enough for my purposes. The main disadvantage is that I need to create a specific one for each component/footprint I use. Once I have the components ready I need a way of holding the components in place when I flip the board.
Recently, I have switched to KiCad for all my designs. The main reason is that the file formats are documented, that allows me to extract information from my boards as I please. Some time ago I created a simple program that reads the position of every component alongside its courtyard and generates OpenSCAD code that renders a platform that I can 3D print. For example, the platform for Wolv is the following.

This program is fitted only for the components that I commonly use, therefore it does not make much sense to release it. However, I may prepare a separate post showing the steps I use so you could implement something similar using your favorite programing language.
Once the platform is 3D printed it looks as follows.

Using the screw holes I can fix it to the board and it is a perfect fit.

Soldering a board in this state is much simpler (as you may have seen in my video above).
Conclusion
So far, these are the tips that have worked the best for me when building modules at a small scale. I will be glad to hear your suggestions if you have anything that can improve my workflow.

How is caudal 2 development going?
Just ordered a Wolv. Really excited to use this amazing sounding wavefolder.