I'm back,  tired of me yet?  The next chapter in the "free bike" saga.

I can only get 1st gear and neutral.  before I put the cases together I had all the gears, and after I buttoned it up I could turn the shift drum thru the gears.  But now that I'm almost ready to start it, the drum will only give me 1st and neutral.  I've taken the linkage apart and pull the index plunger and tried turning the drum by hand.

So, before I pull the motor, do you have any words of wizdom other than sticking to Brit bikes?

What has been mentioned many times on the subject is engine needs to be running for proper engaging of gears. With it on the bench apart you can rotate the trans by hand to get it to shift but once buttoned up only the engine running will verify if you have a problem. Good sign you had all the gears earlier. Don’t fret but get it started and will probably be good. Maybe worst case if still won’t shift just remove clutch cover and be sure shift arm still where it is supposed to be on the drum and double check finger is centered between the pins on the drum.

I have the rear wheel jacked up and spinning the wheel by hand.

one the shift lever, what is the purpose of the eccentric pin that sits between the spring legs?

What model? On some there is a "sector gear" in the shift linkage that can get out of time if shift shaft is allowed to move inwards. Symptom is exactly what you describe.

With more messing around I can now turn the shift drum if I spin it fast enough. But I found another part that was lost and / or not installed. Just ordeered what I hope to be the last part off the bay.

So a brief history of this bike.

A friend whom I will nate, had this bike and sold it to another friend who wanted something for his kid to learn mechanics on.  Somehow this motor was torn apart and put back together.  After which it would not run and eventually was given back to Nate who then gave it to me.  (with title).

So what I found;  cylinder was bored, but one ring land on the new piston was chipped.  The rings was bent and there were no wrist pin circlips.
Collar that sits in oil seal behindd the counter shaft sprocket was missing.
shift drum plunger was missing,  the hole was pumped full of yamabond up to shift drum. and a quarter was glued to the case as an oil plug.
Flat bearing hind clutch was missing.  Clutch, engine sprocket, and rotor nuts weere all loose.
main seal behind rotor was mangled
screws holding case halfs together were mostly missing.
what seems to be half a tube of yamabond smeared all over inside and outside of cases.

I know I'm missing a bunch, but you get the idea.

Free bikes suck, but Ive got a free honda cl350 waiting for me up in Iowa as soon as I can get up there.

Looking back through your posts i worked out its a "72 DT2--250 [not DT250 if you're looking for parts as they started in "74]. But anyway--you asked about the eccentric pin. There's actually two, but the big one is to set the total travel equal both ways so you can get a 20thou feeler between the arms that swing at maximum movement. Then the small one is used to set the short movement each way so the claw arm has the same [or close to it] free travel before hooking the pin each way. Got to really be up past second to third or 4th otherwise neutral gets in the way. Third or 4th 7 nothing in the way to go up one or down one . Not done mine for years. So, two links below, you are talking #14 & i'm talking #9. Now the bent ends of #27 & #28 fully move to within 20 thou each way & come up close to a flat area where you measure & set the gap. As i might've said i've not done it for i dunno 50 years & really if nothing's been damaged then it shouldn't be necessary. But motocrossing them & damage happened back in the old days!!
www.partzilla.com/catalog/yamaha/motorcycle/1972/dt2/shifter-b
www.partzilla.com/catalog/yamaha/motorcycle/1972/dt2/shifter-a
Just for a laugh--& i guess ya all getting sick of my links--here's my DT2 just for you RICHRD--if i can find it. Drag it to 5.10 or just before & there's my DT2 about to dump me off haha. Hope i'm right & yours is a DT2.  

Couldn't link it but hink this should work. Bike #2 orange 'new' DT2. Loved that bike.

I liked those old school mx tracks. or I did when I was young enough to ride them.

AND NOW, wonder of wonders, the bike runs and shifts........ UNBELIEVABLE

but it shows definite signs of an air leak, the petcock leaks, and the front forks are ridged.

on the forks, I tried the old routine of loosing all the bolts and axle and pumping the forks as I tightened evenly with no help. I don't think anything is bent but I'm going to find my fork jig and do some investigating.

Could remove the forks & just clamp the base in the vice then revolve the tubes. Any bend will be obvious. Or if you don't want to go to straightening i'd just [while still in the bike] support the bike on a box so front wheel is lightly touching the floor then turn each tube individually with the axle loose & watch the axle area for bent forks to show up. Then just set them either forward or back [i'd go back if only a small amount] & set them equal as you can get & under no stress pulling sideways to clamp the wheel. Should then move freely. That's providing they're not full of water or mud like we'd get on farm bikes at work & just a mess.