Recently swapped a D16Z6 manual transmission into my 1997 Civic that was an auto and it’s having a weird bounce in idle causing bad shifts and me to lose power

 

The idle drops fast so when I shift the engine rpm isn’t really smoothly connecting with transmission and is also throwing on the check engine light sometimes need help

 

Also sometimes when I try to start my car the battery and oil light will be on (normal) but a check engine light will be on and the main relay won’t click over so vehicle won’t get spark and sometimes it won’t do that