I did a thorough rebuild on my A4 after my wife and bought our E29 in 2005 and sailed her to NC. We purchased the boat in Rock Hall, MD, then made our way down the Chesapeake, ICW, and North Carolina sounds to Oriental NC (400 miles), and had engine trouble the whole way. A lot of the issues were as you described, and rebuilding it, while successful and hugely educational for me, was still expensive. I tore the engine down to every last bolt and part. The shop service alone was close to a grand, which included hot tanking, magna flux, shaft grinding, head/block grinding, cylinder boring, and pressing new cam bearings in place. Then, the parts from Moyer for the rebuild were at least another grand. This included a couple of bigger ticket items including a new starter, fuel pump, and electronic ignition, and I decided if I was going to do this, it would be done right. The long and short thought, was that is still, all told, probably around $2500 for me to rebuild it. It is a great engine and runs fine, but you still can't deny the fact that a carbureted, sparked gasoline engine will succumb faster to marine environment than a diesel, and every now and then I have an issue with the engine underway that needs to be resolved, requiring me to tear down aspects of it to troubleshoot the problem. If I had to do it over again, I would seriously consider replacing it with a Beta Marine unit or the like for about twice that cost. It's a trade-off though, and I'm not saying I would have decided to go that route in the final analysis (or could have expected a troublefree unit from a repower), but I wish I had considered it then. Now I'm committed to A4 - not complaining, and Don is great!!!!!, but since your planing on doing an overhaul, at least look at a repower option.
This is only my advice, worth what you paid for it.