The rules are very clear on this point:
4(h) A minimum of 3 and maximum of 16 segments, including surface segments between any 2 airports, are permitted for the entire journey. Free flight segments within each continent are limited as follows:
Africa 4
Asia 4
Europe/Middle East 4
North America 6
South America 4
South West Pacific 4
(the word "flight" is bolded in the rules)
You have the allowed four flight segments in Europe/Middle East, plus one surface segment there. Your itinerary is fine.
Also, you can stopover in AMM on the second visit. There is no restriction on stopovers, other than being allowed only two in the continent of origin