If, instead of trying to produce terror weapons, the Nazis had decided to put efforts into Jet fighters and trying to regain at least parity in the air, could that have caused the good guys problems?
They did put efforts into jet fighters and they did try to maintain and later regain air parity. The problem is that we were routinely sending raids with more bombers than they had operational fighters in the entire theater.
they simultaneously tried to bomb back the enemy with the V-Waffen.
If no money and raw materials are spent on researching, testing, building and employing those, there will be some surplus potential, don't you think so?
More specifically, I wonder what could have been achieved by completely giving over the resources of the V-2 program to development & production of Wasserfall AA missiles? Since the Wasserfall missile is a scaled-down version of the V-2, it should be possible to transfer those resources directly to their production - the main problem would probably be the guidance system ... (and the fact that a defensive weapon would certainly be less desirable to Hitler than an offensive one)
The problem is that, by mid 1944, Allied armies were advancing into German territory from several directions. Greater German use of jet fighters (which were in fact only slightly superior to, and greatly outnumbered by, allied fighters) and very expensive SAMs like the Wasserfall would have had no effect on the RAF night bombing campaign and only hampered the USAAF daylight "precision" attacks. Eventually Russian and Wally troops would have overun the airfields, radar stations, and missile sites. The end of the war might have been delayed somewhat, that is all.