[Yjisbettr]

Will a stock driveshaft from a 98 tj with d35 work for an 05 with a 44. Would it just be a matter of replacing the rear u-joint?

[bigV]

I'm assuming this is a standard d44 not a rubicon d44
the d35 shaft is 3/4" longer than the d44 shaft and the d44 pinion is longer than the d35's so you will have about 1.5"-2" of added length heading toward the t-case. if the 05 has a lift then it might work - install it then jack the rear end up all the way to make sure it doesn't contact the t-case
if it's a rubicon d44 then no, the driveshafts will not interchange