I have a 99 civic EX, one day it started to misfire and spuder while accelerating from a dead start; seemed to run ok once in the 2700-3000 rpm range. The next day the check engine light came on and it's running worse. I pulled the codes and got the following:

P0705 Trans - Trans Range Sensor A Circuit malfunction (2-posi)
P0706 Trans - Trans Range Sensor A Circuit Performance (2-posi)
P0301 - Eng - Cyl 1 Misfire detected CURRENT
P0302 - Eng - Cyl 2 Misfire detected CURRENT
P0304 - Eng - Cyl 4 Misfire detected CURRENT
P1399 Eng - MIsfire Detected Current
P0301 - MOD $oE Cyl 1 Misfire Detected CONFIRMED
P0302 - MOD $oE Cyl 1 Misfire Detected CONFIRMED
P0304 - MOD $oE Cyl 1 Misfire Detected CONFIRMED
P0300 - Random Multiple Misfire Detected CONFIRMED
P1399 MOD $OE Misfire detected PENDING

I have not done a tune up in a while and I have an exhaust leak that may CAT or above it. Any suggestions on what I should do to identify the cause or where I should start?