Wood floor is thicker than stock steel, therefore the x-members to support it are not as tall as steel floor trucks (floor bottom sits closer to frame). This may explain this issue. NSANE68's suggestion may help. Call the company you bought this kit from and explain what you have, maybe they can help.
Or you could put it back to stock height, put on some steel wheels and dogdish hubcaps, fix the confounded hole in your dash, and be driving.  (This comment added for comic relief and is not intended to dish anybody's project in any way AND it was added after some HELPFUL information)
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Currently on or near the homestead:
67 Chevy SWB 2WD stepside 350/3 on tree (Pat's)
67 GMC SWB 2WD Fleet 402/auto (Brian's under construction)
67 Chevy 3/4 ton 2WD 402/auto (Business Hauler)
67 Chevy 1 ton dually 2WD 396/4 speed (Former business hauler, Needs TLC)
68 Chevy 1/2 ton Suburban 2WD 250 six/3 on tree (Brian's Needs TLC)
70 Chevy 3/4 ton 4WD 350/4 speed (Pat's - Disguised as a 68 GMC)
71 Chevy SWB stepside (Crushed by tree - parts donor)
72 Chevy 3/4 ton 4WD (Parts donor)
72 Chevy 3/4 ton 4WD Suburban (Parts Donor)
72 GMC 3/4 ton 4WD 292 six/4 speed (Mine - Disguised as a 67 GMC)
81 GMC 4WD Dually Dump Body 350/4 speed (Business Hauler)
82 Camaro Z/28 355/Super T-10 (Pat's toy)
93 Caprice 9C1 (Brian's Cop Car)
02 Toyota Camry (Reliable but a souless steel and plastic hulk)
2011 2SS RS Camaro M6 Factory Hurst Shifter 
Maybe I need to sell some of this crap 
Yet another Bozo with a sawz-all
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