Blp952

So I have a 1999 Accord(jap version) and I swapped the f23a1 motor and transmission in it with a jdm f23a motor and trans mission. I'm running into a problem with the transmission not working right in the car sometimes I'll have first gear and sometimes I don't (it's an automatic btw) and I talked to my transmission guy and he said that it's not the transmission but an computer problem. I'm kinda new with Hondas and don't know very much about them besides the research that I have done on them and I don't know if this is the problem and also a side question. Will a jap f23a1 trans fit on the f23a motor and work? Please and thank you in adavance!