6F9 needles are readily available from a Mikuni Distributor like Niche Cycle.  
www.nichecycle.com/6f9-jet-needle-6f09-by-mikuni.html

 

Here's a basic outline based on my experiences.

First rule of jetting:  You give the engine what it needs.  

First step is starting with a known baseline.  Yamaha spent a lot of time and money dialing in the jetting so one of the best baselines if using the stock carb is often the stock Yamaha jetting.  After modifying the engine, I'd simply richen up the original needle and main jet.  Needle by putting clip in lowest groove (raise needle) and main by going up a few sizes.  Pilot jet I might go up a size or two depending on how it starts and idles.  Sometimes I've had to go up on the needle jet if raising with the clip wasn't enough.  Once I'm "too rich", then I slowly and carefully lean out each throttle setting until just below "too rich".  

There are Official Mikuni Tuning Guides here in the Tech Library and all over the Internet, so I'm not going to re-hash all that.  Basically start rich to be safe and slowly lean out.  Critical point is understanding that each jet circuit affects different throttle openings.  Let me repeat that.   Critical point is understanding that each jet circuit affects different throttle openings!  You must know how far the slide is open and make adjustments to the corresponding circuit.  (It's not about RPM, it's about throttle opening.)

It's all in the tuning manual.  But still sometimes people start swapping main jets to try to correct an issue at 1/4 throttle.  I lost count of the times I've seen someone go down several sizes on the main jet to try to correct partial throttle or even an idle richness and then wonder why the engine seized the first time they ran it at wide open throttle.  

In your situation you've modified a DT400 with porting, pipe, and an significantly better flowing filter in the stock air box.  Any of which on their own probably require richer jetting.  All three together?  Almost certainly richer.  (But again see the first rule of jetting above.) 

What you started with was exactly opposite of what I just said.  

Stock pilot = 80. You started with a 40, half the size of stock.

Stock slide needle = 6F9.  You started with a 6DH7.  Again leaner than stock through most of the throttle opening range.  (Stock clip is 3rd from top, I don't recall if you ever said what groove you used?)  



Stock needle jet = O-2.  We don't know what you have, assuming it's an O-2 but that's a dangerous assumption!

Stock main jet = 190.  You started with a 170, again leaner than stock. 

Basically, I'd expect a box stock engine with stock air filter to overheat and/or seize with the jetting you started with.  Yamaha barely passed 1978 emissions in the US with the DT400 and couldn't meet 1979 requirements.  They were already jetted to the edge of "lean" at the factory.  

Finally, you don't actually need to start with the stock jetting.  I just find it to be a huge shortcut most of the time as with mods you normally just need to richen a little.  Jetting requires patience and tedious careful testing.  Start rich and slowly lean.  

Just for fun, I graphed your needle with a needle jet 10 sizes (TEN sizes!) bigger.   That's about what it takes to get close to the stock needle and needle jet.

MarkT you have a wealth of knowledge. I really appreciate your help. 
After replacing the dry side crank seal I noticed I have some up and down play in the crankshaft bearings at the magneto end. I have decided to go ahead and replace the crank main bearings to give this bike the best chance at surviving. I'm thinking there is just enough end play that the new crank seal could be letting some air into the bottom end. 

I have been researching the jetting basics and was caught up in figuring out the difference between throttle opening percentage and rpm range. This bike accelerates slowly enough right now that at wide open throttle there is a flat spot in the middle rpm range. Somehow it's the same rpms that the old worn out 250cc engine was having trouble accelerating. 

The 250 had poor bottom end power and this 400cc engine with a fresh top end has plenty of low end torque in comparison. But somehow mid range burbling is in the same rpm range. Tach cable is not correct or hooked up So i can't pinpoint the rpms where the flat spot is but it sounds and feels just the same. Running the same carb with no change in jetting, same reed valve assy and intake boot on both engines.
I just got the bike together and running well enough to ride 10 min into town with the 250 engine (so i could do my laundry on the weekends because my truck is playing dead) while the 400 cylinder and head were being worked on. 
I hope this mid-range flat spot can be worked over and I'll have a nice ripper to ride around. 

Crank main bearings were delivered today and I'm going to split the 250 cases first to get reassociated with the innards of a single cylinder 2 stroke again. I have built an RD350, a banshee for a friend and a 94 yz250 in th past so I'm confident in my ability, to get this engine apart and back together again. Hopefully I don't feel the need to have the crank rebuilt while I have it out of the engine. I'm really looking forward to riding again. It's been nearly 15 years since I have owned a running bike. 

I'll update when the bearings are in and I'm ready to resume the jetting process. 

Thanks again MarkT

P.s. MarkT I assure you I'm not ignoring your advice. I was just stating what parts I had mishmashed into my carb. I just threw together what I had hanging around, a little embarrassing I must say.. The correct needle is on its way and I'll order another jet kit asap, as well as update you with the needle jet size. I do really appreciate the help MarkT!