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The brown goo is supposed to be there. It keeps the unit from vibrating and making a "singing" noise. Check Bob Robert's website for his "singing" flyback write up and you will see what I mean...
What's the actual problem?
Do you have another machine or board you can try it with? What you're describing could be ground and/or sync issues too!
ALSO when you did your cap kit - did you happen to resolder all the header pins for the 2 little boards that stand up? If not they should definitely be resoldered. Some are tough to get to around the plastic frame but not impossible.