I am looking at put either a 2.5 or a 2.7 in place of the 1.6. Can any one tell me how many modifications need to be done and how big a change to the wiring. Are there and kits out there.

There have been a few guys here that have done that swap, with some documentation too, including pics. Try doing a search in the performance/modify forum. 

There are a lot of electrical changes, and it really depends on if you have the 2.5 or the 2.7.  BRD HNTR did one and is still working on getting the kinks out of it.  The main issue is getting the wiring for the transmission and body control module to work properly and the correct t-case.

http://www.zukiworld.com/forum/build-diaries-how-to-diy/tracker-2x4-rockers-frnt-bmper-4-dr-sprngs-lwered-frnt-diff-$30-steel-frnt-diff/msg217720/#msg217720

We also put in a 2.0L from a 2003 Aerio in Project Trouble for the Zukiworld Challenge races.  145hp and a much easier swap, it will go to your existing transmission and if you get one from a manual you won't even throw any error codes.