95 Jeep Grand Cherokee 4.0

I have a 95 Jeep Grand Cherokee 4.0 that I recently
put a transmission in. It ran fine prior to me putting
the transmission in. Go the old one out and the new
one in got everything back together and double
checked everything. When I went to start the jeep it
started and began to idle rough and backfire out of
the exhaust and the intake. Cps is new everything
works as it should. Any ideas on what may be
causing this would be really helpful. I have put a lot
of time and money into this jeep. I’m gonna be
changing plugs and wires this weekend. I also
checked the timing at tdc and it all lines up and is in
order so timing issue is out. Thanks in advance for
any suggestions/ answers