I got a 98 2500 ext cab long bed planing on a rebuild just wanting to hear some good upgrades to go with that wouldn't put my tranny out of commission sooner than later

 

None. Our transmission suck. The trick is, to be aware of that, and try not to abuse it too much.

That said, I would go in this order:

1 Fix the plenum, and give the engine a thorough tune up. (around 250 or so, for parts)
1a Replace the timing chain and gears. (another 75 or so for parts.)
2 Tuner from Hemifever. (3 to 400 bucks)
3. Harland Sharp 1.7 ratio roller rockers. (325 or so.)
4. Free flow exhaust of some sort. My preference would be the pacesetter longtubes, y-pipe, free-flow cat, if required, and a single 3" pipe to the muffler of your choice, and continuing with a single 3" pipe out the back. (around 500 for the headers and y-pipe....)

See how that grabs ya. Should be good for 15 to 20 hp, and just as much torque. Of course, it's also over 1000 bucks..... and that is just getting started.

1-2 should be done first, no matter what else you do.

 

Got the motor out already was having issues (head gasket) which turned into cracked heads so I got new heads was gonna put them on then I realized I might have a bad lower hearing for two so I'm gonna go a rebuild for sure just wondering about some mild mods to go thru with for some torque if that could be done on the outside of the engine or internally? Transmission was rebuilt not exactly sure when it's got 173xxx on the dash it's always been good to me I just know if I get to much power pushing it, it'll go sooner than later to say the least I expect it just. headed for the motor for now just would like to see another year or so out of it

 

Knowing that, then I'd do everything that HeyYou said, but I'd suggest 1.6 Harland Sharp Adjustable Rockers instead of the 1.7s, a camshaft, and some new valve springs. That should get you a nice bit of torque for that motor.