You may have a height/headroom problem as those furnaces and most are 41" high plus the plenum. You may need to go with a higher end SLP98 which is only 33" high. You need a decent sized plenum with enough height to accommodate a AC evaporator coil. If the plenum is too short you get airflow problems. Sounds like you need a experienced high quality contractor who knows duct sizing and layout. Not something we can walk you thru over the net. http://tech.lennoxintl.com/PDFs/506610c.pdf
"Cut it twice and it is still too short".