I have a 2004 1.8ltr auto that I changed motor in now it does not always start of in 1st gear from a complete stop

It is most likely the transmission, component causing it would be the valve body, which can be replaced separately, but usually if there is higher mileage on the transmission the clutch plates are also worn and replacing the valve body may not fix the whole issue.

When was the last time the transmission fluid and filter changed? I would have that serviced first. If it is an electronic transmission, the line pressure might also have to be reset.

ck trans, fluid to see if it needs to be changed, also replace filter if it has one.

have shop road test and scan possible solinoid

SHIFT solenoid

Auto warning light comes on but goes off when car stopped and restarted. Temp also goes higher

worn shift fork. shifts linkage could be binding.

transmission?

Big Twins clunk too, especially into 1st with a cold motor, even if you free the clutch off first. When I remember, I snick it into gear, pull in the clutch and roll it back and forward to free off the plates. And it still clunks. Sometimes, you will slip from neutral into 1st, almost with no effort, and no clunk and so smooth you don't believe it's engaged (but it is). Weird. I have smooth changes from 4th to 5th and back again, sometimes from 3rd to 4th, but 3rd to second and second to 1st are always a BIG clunk, even if you give it some stick to try and match the revs before changing down. I now go from second to neutral and then into 1st, which is not a lot of fun when you are negotiating a hairpin on Glenquaich at the time... A tighter primary chain seems to reduce the clunk, and there are those who say that auto primary adjusters/tensioners (does a Sporty have one of them?) reduce the clunk. Some disagree... Assume you find it's much better when it's hot..

shifts off electric servo controlled by cars computer , see trans guy you can trust could need service ,oil and filter changed or part , like i said see one you can trust .