The Arduino has female headers. this is wise. you have to work at it to short out things that should not be shorted
modules should have male pins. make female headers for your modules. buy a strip of female headers , a bench vise and a coping saw. saw off what you need, trim the ends with a belt sander. I do this with every module even if I am not sure the module I have is what I need. it takes half the aggravation out of pinning things up.
solder wires to the stubby little pins, hot glue half an inch up, tie wrap the cables together. stress on any one wire will not pull that wire off, and the hot glue prevents short circuits. put a label on each one that is either read from the top, or from one side of the board, so all connectors can be installed properly by anyone with a little common sense
make male headers for the Arduino. same procedure. hot glue unused pins.
pro tip #1: get a copy of freeware Libre office. use the drawing tool to draw your components. I plan to write a tutorial about how to do this in the not too distant future. if you have the same modules I have you should be able to put the modules on a printout of the attached drawing and see only the little L in the center of the mounting holes. ( the Catalex YX-5300 drawing is based on dimensions off the internet, which do not match the reality of the module ). you can move the modules around as you like to fit the board you have to mount it to, to accommodate straight or 90 degree headers, et cetera. you can lay out your design, print it reversed, and use an iron to transfer your design, with mounting holes marked, to:
pro tip #2: you can cut plexiglass or phenolic with a table saw. you can drill and tap either. mark, drill, tap, mount, display the inner workings of your product.
put extra mounting holes on the board for 4-40 & 2-56 nylon standoffs. get the nylon version of a padded clamp, "this clamp is brought to you by the letter P" clamps to constrain the wires and keep stress off the ends, and screw them on top of the standoff.
you get rigid wiring, replaceable modules and Arduinos, and foolproof reassembly, if you don't suffer from malicious fools.
pro tip #3: get wire wrap female headers and make yourself a Proliferator. a small perfboard with 2 parallel rows, 10 pins for power and ground, 2 rows of 8 for I2C. 4 rows of whatever you need for for SPI if you have multiple SPIs. use the little green or blue screw terminal headers for Raw 5 VDC in, Raw 5 VDC out to feed the LCDS without using the Arduino as a fuse, 2 pins for I2C if you have a display separate from the main board.
pro tip #4: those nylon standoffs again. put 4-40 nylon standoffs on your standard issue LCD module. now you can mount it flat on a surface without needing to cut out a hole, or mount it to the front of something from the inside. picture 3 16X2 LCD modules on the left, and 2 20 X 4 modules on the right, of a flat sheet of 1/4" plexiglass. drill and tap one 1/4-20 hole for a camera tripod. bend a sheet of aluminum and drill and tap to mount the LCD panel to your workbench with a C clamp. You have your displays all in one place, all on one plane, handy but not in the way. if you get your act together and take it on the road, put the display on a tripod