Put a strong magnet where the metal fragments "pile up" in the tank. That's where the "swirl" from incoming hydraulic fluid allows the fragments to gather.
You’re not going to like this next comment. I made a post, years ago, about creating a cheap "filter assembly" for the pump/motor hydraulic circuit. Remember, this circuit is NOT filtered by your main hydraulic filter (except when fluid bypasses inside the variable displacement pump…which is why you saw some particles in your reservoir). A catastrophic motor failure is a worst-case scenario for a closed loop hydraulic design. Everything in the loop gets contaminated. If you don't filter this circuit, you will still have a lot of material going round and round. In a commercial machine, they even have ways to drag a device through all the hoses to clean out particles. For a PT, the loop is so short that this isn’t necessarily required. But filtering the loop is, in my opinion. It will take forever for the particles to bypass and get back to the reservoir otherwise. It’s not hard or super expensive to buy the high-pressure filter and other parts. Once you have the filter assembly made, it’s a simple matter to disconnect the hoses from one motor and connect the filter. Jack the tractor up, then use the tram to forward and reverse the flow. The filter design I posted uses check valves to ensure the flow through the filter itself is always in the right direction. Reversing the flow, from time to time, creates a better chance to dislodge any particles trapped in the hoses.
Now, to be clear, Terry will likely tell you to not worry about it. That's because it's a bit of effort to build a high-pressure filter assembly as the parts must be purchased and assembled correctly. Also, ANY high-pressure hydraulic assembly involves some risk because there’s the possibility of a high-pressure leak, causing physical harm. Most companies would not make a recommendation where they cannot control the risk. But, in the far past, PT did offer a filter assembly for this purpose. Also, almost all professional commercial companies will filter a closed loop circuit any time it's opened for maintenance.
What are the downsides to not filtering the circuit? Much reduced life for the variable displacement pump and motors. Now, if you don’t use the tractor that much, and it’s not critical to avoid down time (e.g., it’s not used commercially), and you don’t mind paying for a pump rebuild every 200-400 hours, then you should be good. It’s a perfectly reasonable compromise to make. I’m not making a recommendation…just trying to ensure you have the information to do your own research and understand the tradeoffs.