Can some-one advise me if a RTW permits 3 transits and a stopover in one city or is a stopover also counted as a transit. I have a TA, being told I think by AC, that I can't do 3 transits plus a stopover in one city. The rule clearly permit up to 3 transits and permit 1 stopover. I can find northing that says a stopover is also a transit.

Advice, the answer and a reference link to rules that may answer my question would be greatly appreciated.

They are correct, you can only do one stopover plus two transfers or three transfers in any one city. See it this way, you are only allowed to visit any one city three times and the stopover obviously counts as visit as well.

The rule states transfers, not transits and they are totally different animals.

IATA speak 101 :

TRANSIT - a change of flights at an airport (ergo City) within a small period of time. (Usually within 24hours for International through fares/tickets - less for some domestic/regional connections by some carriers)

TRANSFER - best described as any visit to an airport (ergo City) be it for a transit or a stopover

STOPOVER - an airport (ergo City) stop where the time between arrival flight and departure flight exceeds the maximum allowable time considered for a transit. (See above).

So when the rule says a maximum of three transfers per City, that means you can visit that airport/City only 3 times per journey and then only 1 of them can actually be a stopover. You can do 1 stopover and 2 transits or 3 transits maximum.
On the RTW's/Circle's you can get creative and have 1 or 2 extra overnights in a airport/city if you need to once the one permitted stopover is used up. Arrive late, overnight, do meetings or whatever the next day and get out of town before the 24 hour period since arrival is up. This keeps it as a transit but still uses up one of your 3 permitted transfers.

Cheers.

Can I do an open jaw and a stopover in one city? Could I leave from one city at the end of an open jaw and come back to that city for a stopover?

No. Because an open jaw creates a stopover at each end (but only counted as one total). So when return to the same city you have already had your stopover there.

KiwiFlyer has answered that, but it appears you are trying to work it so you can get a second stopover somewhere. Perhaps if you listed your desired itinerary, some can offer suggestions for you.
Cheers.