I'm not a heavy LAStools user but here are some more universal tips/principles that have helped me.
1) Uniformity with points is a nice concept but somewhat artificial. Example is with model keypoint algorithms which thin points where slope or elevation changes are minimal (according to user settings) but retain density where otherwise necessary to more accurately reflect terrain changes. You want elegant accuracy not strict uniformity.
2) I always look to utilize parallel flightlines and avoid perpendicular unless absolutely required to fill data gaps. Calibrated flightines/aligning strips that are parallel is a much more straightforward process because it mostly involves correcting roll in the platform. Perpendicular complicates unless it's strictly for providing some data for the correction algorithm. I include a single crossing flightline for the Terramatch routine just for that reason.
3) Matching/calibrating/aligning flightlines is absolutely necessary for accurate data. Bayes strip alignment,Terramatch, or some proprietary software can do that whereas as far as I know LAStools doesn't have tools for that yet.
4) I always cut any overlap AFTER calibrating flightlines. Who needs the extra points and unnecessary file size? With correct settings any shadows or gaps are filled with data from adjacent lines. And lines should match by then at the seams. Otherwise as you noticed the DEM will reveal it.
Hope this helps. Good luck!
Mark