I think I might have figured it out. Maybe not entirely though. I will send my configs when I get home to my computer. Basically the rate at which the kerosene and lox are being consumed isn't the same as the original ksp. I adjusted it in the config to match the RO config and it seems to work better. The engines were definitely shutting down on their own due to lack of prop. This last go I was able to get up to about 65km and a speed of about 1600m/s with a little fuel left over (killed the engines myself to try and see if I could do a landing attempt). What was happening before is I was still showing 13k units of ox and about 11 of fuel but the green bars for the engines were empty. How can I send you my configs?
kart- negative on using RO. Was trying to just make the F9 you have work for real solar.