The YB-49 was a YB-35 modified to install j35 engines so there were no YB-49s with R-4369 engines. The YB-47, basically a contemporary to the YB-49, also had J-35 engines and the B-47 later received the J-47, so, I think the J-47 was not ready for the YB-49 and I suspect there was no eagerness to upgrade the YB-49.
There is no doubt that the aircraft with the most potential for handling the future mission of enemy penetration was the B-49 due to its inherent stealthiness. The B-36 was obsolete when it became operational, only one year before the MiG-15 entered service and we know what it did to the B-29 force in Korea.
Performance comparisons using corrected NACA data (as stated in "Goodby Beautiful Wing" by Terrence O'Neill).
B-35 - B36
Empty wt. lbs 89,000 - 133,800
Wt. Cruise 135,000 - 212,000
Wt. Gross 180, 000* - 287,000 * weight reduced from max due to AF refusal to test landing gear
wt. max T/O 207,000 - 311,000
Miles-to-target 5,100 -3,600
Speed Combat (mph) 405 - 331
Design Ceiling ft. 49,000 - 40,000
Note: these B-35 numbers are using NACA corrections to previous flight test estimates using N9M reduced scale test aircraft. B-35 had the potential of performing the same mission as the B-36 at 60% of the weight.
Note also: That the B-49 radar cross section could have easily been improved significantly by moving the engine inlets to top of wing ala B-2. No need to make sophisticated ducts because there would be no airborn radar platforms above it probably well into the '50s, if not later. The B-49 could be practically invisible from the front to Russian radars.