1 Can the Red Army defend effectively against an advance to Moscow itself?
At that point no. The extra time the diversion to Kiev took gave the USSR more time to prepare for an invasion of Moscow. The armies that did stand in the way in the OTL still got destroyed but some inflicted enough casualties that many German units were combat ineffective afterwards.
Can the Germans effectively defend against the Red army grouping against Kiev which will likely mount a magor counter offensive at some sta\ge against that vulnerable German flank
Yes, these groups were not very well mechanized and even without the encirlclement, the Russian railway system would've been overburdened with both Moscow and Kiev as a priority. Stalin would've undoubtedly focused on keeping Moscow supplied at the cost of Kiev. The distances are so great in this scenario that the German could've easily let any such counterattack proceed for even 100 km and still been ok. The russians would've undoubtedly been exhausted by that point and been easily destroyed.
War is logistics and until the Soviet army was adequately supplied with all-terrain studebakers from the US, they could simply not attempt the kind of aggressive attack we saw later in the war and that was the level of logistics required for the Kiev pocket to be a viable offensive force.
With an Operation Typhoon mounted in early September can the Wehrmacht get to Mosco before the Mud Season (in OTL they got to within a few miles of the city even with the lousy ground conditions
Maybe. Weather worked against the Germans in two phase. First there was the mud season which slowed their advance. After which the ground froze and they were able to make substantial gains again. After that there was the terrible freezing which really destroyed the Germans. Their tanks wouldn't run and their guns wouldn't fire. This weather completely destroyed any advantage the Germans had in training, mobility, and organization.
It was at this point they took their first massive casualties of the war: around 750k Germans were casualties when the Soviets launched their winter counteroffensive in the OTL. I think it was actually at this point and not Stalingrad that the war was lost for the Germans. And it was at this point, that Hitler was clearly and obviously proven to be an incompetent and cruel man. When he hard about the weather at the front he went on some stupid story about how he was easily able to deal with cold weather as a kid. This was at a time where men who had lost limbs to frostbite were returning from the front. He acted as if it were simply a matter of willpower.
4 If the Germans get to Moscow should they ncircle the city first or directly storm it/
They should encircle and storm it. They would take casualties but if they were able to cut off the city, the entire soviet front would be paralyzed. Moscow was the central railway hub for the entire Soviet union and cutting it off would've rendered logistics almost impossible for the lines as they stood at the end of 1941. All soviet fronts would've had to retreat many km if Moscow had been taken.
5 Does Moscow become a Stalingrad style urban battle pulling in more and more German units
It is hard to say if casualties would've been at Stalingrad levels. Soviet morale was at an all-time low at that point and Moscow would've been poorly supplied and equipped if the Germans had moved faster. You can cut Moscow completely off with Panzer encirclement whereas Stalingrad was split by the Volga and so the Russians were always able to supply from their base across the river. At any rate, the casualties to take Moscow would've been worth it given Moscow's strategic importance. It had about 15% of the industrial capacity of the USSR and was THE central railway hub for the entire Soviet Union. Losing it would've made logistics extremely difficult for the Soviet army.
If the Battle of Moscow does become a Stalingrad style battle does this make the Soviet winter offensuive more effective?
The Soviet Winter effective was largely possible because the 18 or so Siberian Divisions were moved by Rail and deployed right to the front at Moscow itself. Without Moscow as a hub, they would've had to been deployed several hundred km inward which would've made the winter offensive much harder if not impossible.
7 If the Germns do take #Moscow how likely is it that Hitler wins the Russian war through Soviet collapse (eg a Gneral's coup agains Stalin?
It is hard to say. Stalin had purged the military so brutally that even during the darkest days of the war in the OTL his position was largely secure. And even if the Germans had taken Moscow, they would've done it with little time and men to spare. Both sides would've been severely outside the reach of their supplies at that point if Moscow's railway lines had been cut. The German supply position was terrible but so would the Russian supply position at that point. I think there's a serious chance that the Soviet winter offensive might've been effective at pushing the Germans out of Moscow anyways.
The most important turning point after the fall of moscow was whether Leningrad would've fallen. If the Germans were able to capture it (it would not have had moscow to help supply it), then they could use the railway line to supply their moscow garrison. It would've made the supply situation much more tenable for the Germans. Leningrad was also responsible for about 15% of the industrial capacity of the USSR as well. In the OTL, the Germans had taken about 40-50% of USSR industrial capacity and population at their peak gains. The twin blows of Leningrad and Moscow fallen would've put the Soviets in a terrible place.
The fundamental problems with Operation Barbarossa was that Hitler was an idiot that didn't understand military strategy at all and secondly the logistics/production of the German economy. The Germans really had no plans to adequately supply or provision their troops should they capture their objectives anyways. The rail lines did not extend far enough and the railway gauge of the Soviet Union was completely different from the Germans. Not only that, they had not stockpiled enough oil for a long campaign and even more arrogantly, they had actually decreased arms production during the fall because they expected the Soviet Union to fall. They didn't even produce enough tanks to replace the 25% or so tanks the Germans lost to simple wear and tear during their early massive victories.
So even with a victory at Moscow, so much else has to go right for them that it is unlikely that it changes the final outcome, though the war might've lasted a year or so longer on the eastern front and the iron curtain would've been farther to the east if they had been successful at Moscow.