Non woven geotextile fabric for french drain clogging in heavy clay
You want water away from your basement wall and your solution, which often works, is indirect, you're attempting to drain all the water away, rather than the water you care about. 

A solution is to keep the water away from the exterior of the basement wall using a waterproof coating on the exterior of the wall, and then a drainage board over the coating. Then, set up your foundation drain to drain the water AFTER it gets through the filter covering which is outside the drainage board. This eliminates the clogging issue. If the filter clogs, you're happy because the water isn't getting to the basement wall.

For the other issue, treat it separately by continuing the non-perf pile the entire distance.