there is LONG treatise at the 700/900 FAQ on these questions and even a cursory search here will yield reams of info. nevertheless to be brief


Need some advice
1.Counterhold tool when put on turns tdc off a little is that normal?

not an issue

2.Do I need to remove valve cover to change out cam seal?

no

3.What else besides cam gear needs to be removed to put new back cover on for
timming belt cover?

cam sprocket
intermediate shaft sprocket
crank sprocket

4.Have checked flame trap componets seem ok ,

5. How do I change out intermediate seal ?

same way you change crank and cam seals, with the same seal puller

6.How do I know intermediate is lined up cannot seem to see mark with bottom cover on.

take off diz cover and see if rotor is pointing at # 1 plug wire as it should