Think how much pressure is generated in the cylinder by the upstroke. The crankcase has a lot more volume, but those pistons moving down still compress air and create pressure. I've never measured it, but I'll bet it is somewhere around 10psi or higher.
When you put that filter on the end, you created more back pressure without a doubt. Plus, anytime a tubing run takes a bend, it creates restriction to flow and that creates back pressure. Add length to a tubing run and that too add additional back pressure.
I agree that the set-up you show looks restrictive to me. I would come off the primary vent pipe with something that allows you to vent into the biggest tube you can find, if you want to run a straight vent. Better yet, if you put a PCV valve as was discussed here a year or two ago, you will create zero to possibly negative pressure in the crankcase and that does two things. First, it will suck instead of blow so leaks that currently exist due to pressure should stop. Sucking is good in this instance. And, with a vacuum in the crankcase, you'll reduce pumping losses so you'll gain a little HP.
Search here for crankcase vents and PCV valves I'm sure you'll find info. I think Gatornapper put one on his bike.