The 6th Bomb Group

A squadron of Franks attack B-29s
Painting from box art of Tamiya 1:48 scale model.

The Ki.84 was one of the planes developed later in the War that was capable of climbing to meet the B-29s. It proved to be a deadly opponent:

When 27 B-29s of the 6th Bomb Group struck Tokyo on the night of May 25, Sasaki took off in an unmarked Ki84-1-ko. Flying above the American formations, he would select a target silhouetted against the burning capital, then dive at it head-on. In that manner, he was credited with shooting down three B-29s that night (the 6th Group actually lost three planes, plus 14 damaged).
[John Guttman, "Last Deadly Gale from Japan", Aviation History (May 06), p. 22, 58]

Ki.61 fighters of the 244 Sentai in front of Mount Fuji.
The aircraft in the foreground is flown by Group CO Cpt Terohiko Kobayashi.
On 27 Jan 1945, Kobayashi used this plane to ram a B-29.

Like the P-51 Mustang, the Kawasaki Ki.61 used an inline water-cooled engine.

This shows the altitude of the various AA guns.

The Japanese had several different types of anti-aircraft guns.  Some were fixed in place. Others were mobile and could be moved where needed.

An acoustic target-locating system.

At the beginning of the war, the Japanese used visual and acoustic aiming systems. By the time the B-29s attacked, these had been converted to radar-directed aiming systems.

The Type 99 was a copy of the highly successful German 88 - known on the Russian front as as the "crash-boom" because the shell hit before the sound of the gun arrived.  It could shoot high enough to bring down a B-29 at almost any altitude and was produced in large numbers.

Caliber: 88 mm (3.46")
Shell weight: 9 kg (19.84 lbs)
Muzzle velocity: 800 m/s (2,625 ft/s)
Altitude: 10,420 m (34,186 ft)
Production quantity: 500 - 1,000

A German 88 in action

The Type 3 was designed for air raid protection.

Caliber: 120 mm (4.72")
Shell Weight: 23.4 kg (51.59 lbs)
Muzzle velocity: 853 m/s (2,799 ft/s)
Altitude: 14,000 m (45,931 ft)
Production quantity: 120

The Type 5 was a monster. It could hurl a 110 lb shell into the stratosphere. Fortunately, the Japanese produced only 2 of these guns in August 1945. They were located in Kugiyama, a suburb of Tokyo and brought down 2 B-29s in a single engagement.

Caliber: 149.1 mm (5.87")
Shell Weight: 50 kg (110.23 lbs)
Muzzle velocity: 930 m/s (3,051 ft/s)
Altitude: 19,000 m (62,336 ft)
Production quantity: 2