When installing my transaxle, I had several hours of trying to line up the tranny to the engine... well.. for anyone wanting to know the way i got mine on... heres how.

First...raise transaxle to height just a little lower to line up the input shaft with the clutch splines.
Once the input shaft is on, push back until seated.
Alight the transaxle so that the right locater pin is in its housing 1/2 way.
Then push the right locater pin all the way back until it is about seated against the engine.(It wont seat all the way because the other side isnt seated.)
Then get someone to watch as the left locater pin lines up with its housing.
Take a bolt closest to the left locator pin and put it through the bracket from the engine to the transaxle and thread it through and watch as the transaxle pulls closer to the engine and as the locater pin pulls into the housing...
Then, fill in the transaxle to engine bolts...(torqued)
Then, put all the bolts in the brackets... (torqued)
Lower jack... and do all the other stuff you need to do to get your Honda running right again :D