Some thoughts on your problem...
When you had the Timing cover off, did you inspect the Timing Chain and the Tensioner. (#16 in the diagram below) If there is too much wear on the tensioner it can cause slack in the chain and the timing to be off. ANd experience problems like youre talking about. When added load is put on the engine it seems to go away. Depending onthe previous owner and the frequency of oil changes, the faster the tensioner wears since its nothign but a plastic guide and a metal chain.
Some other thoughts would be to do a compression test.
Also to check the ignition system, you may have a split plug boot or a coil thats starting to fail.