If you trust your filter, then by all means use it. The cap tube is a predictable metering device with no moving parts. If it clogs, you can tell pretty easily. If it does clog, just chop off a couple inches (as you did) on the high-pressure side. Contaminant will lodge in the upstream end pretty quick if it is going to.
Watch this and be well informed:
No matter what the scientists tell you, cap tube sizing is a trial and error affair. With a perfect charge, with brand new everything, a calculated value will get you somewhere in the operating range. Where in the range the unit works best depends on many variables that change against each other when you shorten or lengthen the cap tube. This includes the system charge.
With a manufactured unit, this allows the designer to rapidly prototype and optimize a unit that can be blueprinted once and be copied easily. At the factory, they build it to the print, weigh in a charge from deep vacuum, do a quick function check, then It's done. Nothing to tweak, so the thing does what it does consistently until something breaks.
What this means for you is once you get the cap tube optimized in your running range, there is not much else to optimize. Making some test runs after a major change (cap tube or charge in your case) will provide the key performance indicators to tell you if what you changed did any good or not. Just make sure you take enough readings and notes while your rig is in a certain configuration. You may reach a point where you went too far and want to backtrack.
From your posted testing, you have increased your heat flow by a substantial amount by removing just a short piece of your cap tube length. I don't imagine you will have to remove much more before the compressor finds its happy place.