Rommel conquers the Nile delta in the early summer of 1942, due to whatever it is which Germany does differently (Rommel wins what was in original timeline first El Alamein?); British lose Malta and all credibility with the Americans; Roosevelt insists on landings directly in France (what, as far as I remember reading (maybe wrongly?), he originally wanted) and British don't have any credibility to say 'no'; Allied landings go in in France and go disastrously wrong; Britain between North Africa and France now have no army left for use in Europe; Allied amphibious lift capacity has been gutted (setting back all future amphibious attempts) in the failed French landings; Vichy France is still a thing and still pro-Axis; Italy is still in the war after mid-1943; all Hitler has to do is worry about the United States Air Force in the UK, bomber Harris' 'dehousing' attempts, and Russia, until American atomic bombs start to drop on Germany.
(Best I can do. Requires yet more rolling maximum on dice by Germany, and yet more idiocy by British. Possibly borderline Alien Space Bat, but the Germans - by actions such as being more careful of their SIGINT in Libya - might be able to preserve at least some of their enormous early 1942 desert war intelligence advantage over the British.)
Germany slowing atomic bomb progress by much after 1942 is it seems to me probably not plausible. Germany is on the wrong side of the Atlantic to do much about the project.