i just did a full rebuild on the engine and swapped out the transmission on an 89 accord lxi. before i pulled the replacement tranny, we tested all the gears for shifting and sound. after install i don't have 1st and 3rd, and 5th is difficult to hit also. there is a sound like the shift lever is hitting under the boot. the tranny is the same model # as before, and i don't see any way to adjust the shifter. i haven't installed oil into the trans yet, but i did adjust the clutch. i'm iching to start the new engine for break-in, but i need to sort this issue out first.

 

Sounds like it is not aligned properly, did you replace the trans and motor mounts as well?

 

i did install new motor mounts. the issue seems to be along your line of thinking, but i won't know untill i pull the exhaust to see the shift linkage under the cat converter. the torsion bar, where it mounts to the tranny, is about 1/4" to long, and i just took advantage of the rubber mounts to gain that leverage. and when I try to shift into 1,3,5 the tranny pushes away. i'm thinking i need to shove the engine tranny 1/4 to 1/2" away from the firewall. i'm not sure how to gain that much movement, but i'll see what i can do.

 

I had the exact same problem in my mustang years ago and the transmission mount was torn. Replaced it and was fine.

I also had problems in a Jetta where it would grind going into gear if you were kinda hard on it. Found two problems: 1. transmission mount and motor mounts bad. 2. There was mounts that connected the front under chassis to the body, those went bad.

 

the cause: a hump shaped metal cover that holds the backside of the torque rod was being hit by the square block build into the shift rod under the gearshift lever.
solution: i lifted and "nudged" the engine away from the firewall and retightened the motor mounts when i was as far forward as i could be. that gave me 3 & 5th gear, and 1st slightly hit by about .02" i pulled that metal hump-shaped bracket, grabbed a drill and enlarged the mounting holes about 1/8" slapped it together and it functions correctly.