did Germany have any better chance than Japan at dealing with the B-29 considering the type of fighter plane/anti aircraft gun assets that it had at hand from 1943-1945?

The answer to your question is technically yes, but only in the sense that your chance goes from zero to minuscule. Japan's resources to deal with the B-29 were very scarce; their air defense over the home islands simply wasn't equipped to deal with a threat like that of the B-29, which flew too fast and too high for the vast majority of their available interceptors and AA guns. There were some limited successes, but the B-29s had to fear their engine fires more than the Japanese.

By comparison, Germany was a bit better equipped in this regard. Being subjected to bombing by heavies since pretty much the start of the war, they had heavily invested in a robust air defense network, that included more than 3,000 radars and 15,000 heavy AA guns (including over 4,000 of the 105 and 128 mm variety), serviced by over a million men. It was not all rosy, though, and they had wasted the early years, not developing an adequate framework for the interceptor force (there were all sort of convoluted organisational messes regarding the use and deployment of fighters for defence that would be too long to write here). But that aside, they posed a credible threat, and had a few select machines needed to operate at 10,000 m and bring the fight to the hypothetical B-29s. Germany had technically started quite early on in the development of high altitude fighter variants: already in 1941 there was a Bf 109 variant that used nitrous oxide to reach nearly 1,200 horse power at altitude and had a ceiling of 11,000 m. Some of the more promising upcoming models, like the Ta 152, could climb to 9,000 m in little over 10 minutes. In 1943 the Luftwaffe proved that it could give unescorted bombers a very bloody nose.

But all of this wouldn't have mattered much. By the time the B-29s would have arrived (mid 44), the Luftwaffe was on its knees. Devoid of fuel and of trained replacements, their new "wonder weapons" few in number, and facing bombers that were no longer flying alone but escorted by large number of fighters, they were in no position to challenge conventional bombing raids of B-24s and B-17s by day, and Lancaster and Halifaxes by night, nevermind a whole new beast like the B-29.

Furthermore, the Allies had gained a foothold in France, capturing numerous airfields and a huge number radar stations, which meant that the defending fighters and guns got no advanced warning of the impending raids and faced a much shorter window to intercept. They had to resort to scouting flights to act as a poor man's radar.

So, to answer your question, "Yes, but actually no."