sounds like you had a combo of previous ownder bodges + airlocks, my thermostat was cut out in exactly the same way, when I put a new one in it ran absolutly fine, so the only reson they had removed it was to save the cost of a new stat, how tight is that?!?
In future when you drain & refill the coolant system bleed it by running it from cold with the cap off, keep the level topped up. Rev the engine to 2k now & again, and the whole time grab all the hoses you can lay your hands on & squeeze, dont forget the heater matrix ones! When the hoses get too hot to touch or the coolant starts boiling switch the engine off and fit the cap. Never fails!
No need to set the heater to hot on a MK2, as the matrix always gets coolant flow. On a MK1 there is a valve that isolates the matrix from the system. Also when you rev the engine check there is a good flow of coolant out of the small pipe to the top of the matrix, if not its blocked or your waterpump is weak!
