An 88 inch twin cam sitting on the side stand would not empty the oil filter over time just from sitting. Something is not right , I wouldn’t start it again untill you figure it out. If you had enough metal in the oil galleries to block the filter lines then your motor wouldn’t sound too flash. Sumps on the bottom of those and it holds about 2.5 quarts, what did you drop out? How much crap was on the magnetic drain plug?. How many miles on the motor, reason I ask is 03 models still had the spring loaded cam chain tensioner arrangement which was changed in 06. The tensioner shoe is under a lot of pressure and they have a fairly limited service life about 50-60 thousand kilometres, what ever that is in miles. One of the issues with that system is if you let them go too far past the service interval the shoes can shit themselves and the resultant chunks of the shoe can get sucked into your oil pump and block it. Not good.
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