trans will fit phisycally. But your 99 speedo will not work with senser on T45 from pre99.
And H pipe.... i owuld not think it'll fit, as 99+ and 96~98 usualy have different part number
i think i remenber reading it somewhere that u can swap speedo gear thing around. But unless u know what you doing, i say thats peofessional job.
as far as swap goes, its not mechanical driven speedo. its jusy mechanical pick up. it still goes through ECU. so if u want to swap gauge out, u might run in to more headach like your PATS not workin and such...
Cobra's have a different tailshaft then a Gt, so it wont bolt inplace unless you. 1 remove and use your Gt ext housing. or 2 cut, relocate and weld the trans crossmember support brkts in the correct location.