The original fuel filter on the carb' MK3 is in the tank attached to the pickup line it is very small and if there is rust or debris in the tank it blocks very quickly. The best way to solve this or to check is to remove it from the tank and fit an in-line filter in the flexible hose within the engine bay (a clear one to see fuel flow easily will be few pounds from a motor factor).

Try cleaning the cone shaped crank-case breather filter under the air filter box or remove it to see if it helps it run smoother. Cannot be fully sure but the breathers can cause similar issues to those you describe.

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Another thing that happened to me was something like a loss of oil pressure - I think - this happened during a long run where the engine just shook for a period then lost power (preventing tappets pump up (?) leading to loud tapping from the top end). It resulted in a new engine. Though not entirely sure whether it could have been a head gasket failure (I was a novice mechanic at the time).

Let us know how you get on.