Will the 2.6 motor bolt up to the 2.3L 5 spd trans? If not how hard is it to swap the trans? the 2.3L trans is cable and the 2.6 trans is hydraulic correct?

there is alot of differences in the transmissions. one is what you pointed out. the 2.3L has the cable clutch on the driverside, the 2.6L has a hydro clutch on the passenger side. The 2.6L clutch assembly and flywheel are BIGGER then the 2.3L. putting a hydro clutch set up in a pup is alot of work, firewall has to modded to bolt up the master cylinder. IIRC, you can use the trans plate off the 2.3L and put it on the 2.6L motor when you put the pieces together. use a stock 2.3L flywheel and clutch or upgrade the clutch though only a 27 hp gain shouldnt be needed. the trans plate helps keep the cable set up working. good luck