Sounds like you may need to adjust your Bowden cable and/or check your vacuum going to the VCV on top the IP and to the trans. Check the vacuum before making any adjustments. Hard shifting is a sign of low vacuum. Higher than normal vacuum will cause softer shifting or flaring. Hopefully Brian Carlton will chime in here. He is sharp on trans settings. (Along with many others on here) You will also want to make sure you have bypassed the 3/2 valve on the valve cover and bypassed the EGR system (for testing purposes only of course) to help eliminate the source of any other leaks.

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2005 Accord Hybrid (Wifes)
1995 Subaru Impreza L AWD (Snow car)
1984 GMC Sierra 1500 (Mine)
1983 300CD Best $ I ever spent. (Mine)
1984 190D (sold and glad I did)
1983 300D (sold and wished I hadn't)