1) What do you do with the ecess/other vacumn lines? Do you transfer all the things from the acura firewall to tha honda or do you just like plug them off?
Use what fits. Some vacuum line maybe longer, shorter or teh same, usually you leave the firewall stuff alone, ei brake vacuum hose, heater hoses etc..only one you may need to mess with that I can think of is the MAP if it is mounted on the firewall.
2) If you doing the change over from hydrolic to cable transmission ... would u use the whole petal brackets from the integra? not to sure about how that works. (any ideas would help)
Civic pedal set is fine, no need to make extra work. The conversion converts at the slave cylinder.
3) We swap the transmission mouting peice from the teg to the honda correct?
You mean the mount? Yes.