So I've got a 99 ctd...intake, exhaust, juice w/attitude and other little crap, soon to have injectors as well.

It has 125k on the odo and a transmission that shifts great...
I'm still afraid to put it on setting "5" though. I don't think that I can afford the full on ats trans right now or in the near future, what I was wondering is if it would be worthwhile to throw an upgraded torque converter and valve body into the current trans and run it until it dies, then possibly try to buy a valvebodyless/tcless trans from one of the performance companys or maybe even a stock rebuild trans with the upgraded tc/vb? I probably won't go much more than the injectors and possibly meth/water injection in the future and don't tow more than 7k lbs. What do you all think?

Also, with the tc and valve body, I have been going back and forth between ats and BD...any opinions?

Going with a VB and TC would definitely be a good start and the way I would go at this point if I were you. Keep in mind that the inevitable will happen at some point though.

You might try calling Goerend transmissions for the converter and valve body. I've heard other people say that they are pretty easy to work with if you already have some of the parts and then call up looking for a whole tranny. He also stands behind his products. I've got one of his converters in my truck and have been very happy with it. It has a lifetime warranty on it if I screw it up too.

Have you ever considered building your own transmission?

I put a TransGo shift kit in my 2000 CTD when I had it and I had no issues when I had my Edge Comp cranked up, I had an intake, exhaust, the Comp, and RV275 injectors. The shift kit made a BIG difference in mine. I had plans to upgrade the tranny as well, and this was a fix to hold me over. Cost me ~40 bucks for the kit, and a few hours to do it.