You can order the body and clear parts through Japanese online shops like HW Japan, HLJ, Hobby Search or Rainbow Ten. Use the part numbers for the Hilux Double Cab Lowrider that is recently re-released:
http://www.1999.co.jp/eng/10080779
For instruction manual, Hobby Search might have them in their web site. Find a recent release of the Hilux that is closest to your kit.
http://www.1999.co.jp/search_e.asp?T...=0&itkey=hilux
Wheels and tires will be tough, the stock ones are long out of production. You might try ordering the ones from the other Hilux kits.
If you order all the missing parts, it could cost you more than buying an entire kit. But it doesn't hurt to give it a try.