Turning the jets down gives MORE gas, Yes there will be a slight reduction in air when you put the filters on but not enough to give trouble at this stage. Don't know what filters you're using but I hope they weren't damaged by the fire. That could really block them up. You need to start from scratch with the tuning, back to basics before you even try and start the engine.You can use your Uni-Syn (Unidine) after you get it running to equalise the flows. There are several good how tos on the net re tuning SU's. I hope Phil doesn't mind me posting the link to his.
http://www.vclassics.com/archive/stoichio.htm

John Twist at University Motors has several on YouTube which are worth watching.
Start here http://www.youtube.com/watch?v=7GRAcqDySog

Lots of others on YT from other sources as well.
Yes SU's are a simple carb but they need setting up step by step to get the best from them.