Thats way low. My 2000 when stock like 100% stock made 296hp and 318ft/lbs. Added a cutout only and went to 301hp forgot what tq. Best E.T. at San Antonio was a 13.13@107.99mph 2.73 gears w/A4 cutout opened. 13.29 closed.
Are they the 98 Head casting? I am guessing the tune is the devil here.

 

Start with a compression check. Then fuel filter and you said plugs where fairly new right? If all that comes out ok time for a real tune.How many miles on it? Also how new are you O2 sensors? how long ago did you do the long tubes? Also what O2 sensors are you using?

 

fuel filter fuel filter fuel filter

 

Are you leaving in second gear? No kidding my friend was doing this and was like "man why am is my **** so slow" and sure enough...leaving in 2nd.

If not, seriously check your ride out with routine maintenance. Stock cars should at least run 13.5's

 

As others have mentioned AFR... when you were on the dyno did you get an AFR printout? Mail order tunes assume proper operation of all parts. Aging MAFs can report low and cause the car to be too lean. Tuner's can easily spot problems like this in person, or you can yourself with a wideband. Also, if you DO have a dyno graph with wideband, most any tuner would be happy to take that and your PCM and get you updated.

 

my stock 99 ta was stored for two years before i bought it, it ran 15.2! i changed the air and fuel filter and cleaned the maf and it dropped to 14.1 still working on launching my m6.