There is no simple, single solution. There are multiple things you could change, but every change has other possible knock-on effects. Mass changes are not usually a great idea. So tweak and see if it gives you the result you are looking for.
Your fundamental problem with defending is a lack of players back to defend. Most IFs are not gonna track back that much, so if the opposition attacks a wing, they can potentially be doubling up on your lone fullback on that side. That makes it highly likely they are going to get the time and space to put in an effective cross. And when that cross comes in, you only have the two central defenders, and maybe the opposite fullback. Any runners from the opposition midfield are gonna come in probably unmarked. If they have 2 or 3 players in the area and you have just 2, that becomes a cross with a high probability of success. You may also be somewhat susceptible to thru balls without a DM, especially if the opposition uses a playmaking AM. You are almost always gonna be outnumbered on a counter attack because your front four won't come back enough and the two CMs may not be in a position to. Especially with roaming.
Some options:
-have a DM. Adds defensive solidity. Probably swap the AM for a DM
-have your IFs specifically mark the opposing fullbacks. Or have them as ML/MR, which will naturally defend a little deeper and would switch it to a 4-4-1-1 (unless you also move the AM). The IF role isn't naturally available at ML/MR but you can create it with PIs. If you drop the wingers, you could even up the FBs to WBs to have them a bit more attacking.
-don't get caught up on "preferred roles" too much. If the player has the skills and PPMs to make them effective in the role, they should do well, even if the game says they aren't ideal for it. Be reasonable, obviously. But a personal example - I had a mediocre striker (for the league) playing as a Complete Forward, despite the game saying it was his worst role, and he was hitting a goal per match on average because he had key skills and it fit the overall intent. And that's the important part - the roles and duties need to fit the tactical approach more than they need to fit the player.
-you have a lot of Team Instructions. Like, A LOT. Probably more than necessary. I tend to look at TIs as tweaks. Outside of a few that are going to be required to create a particular style of play (pressing, for example), they should be added when the base tactic isn't doing what you want in that regard. Think about what you are trying to accomplish with each TI and also what negatives they might be bringing. They also stack. So having short passing in addition to Retain Possession stacks and can be too much - the will simply look to hang onto the ball to much, not really getting into good attacking positions. I would drop Retain Possession, Pass Into Space (use it if you are being pressed), Play out of Defense, Look for Overlap, and Roam from Position. These could all be adding unwanted negative side affects. Part of the problem with play out of Defense combined with the short passing is that you might be limiting your options. When a central defender has the ball, how many passing options do they have within their passing circle? Other defenders. MAYBE the DLP, less likely the CM, almost certainly not the IFs or AM.
