We can Do a MMR 600 with New Pi heads (longBlock) for around $3300. That will support up to 600 rwhp.. I think this would be your best bet. For the future it gives you room to grow if u choose.. LET ME KNOW IF I CAN HELP.
You will need intake adapter plates, a motor, a 8 bolt flywheel and about 2-3 days. It's a direct bolt in for the most part. Search google for "5.4 swap mustangboards" and you'll come up with my bigazz thread. All questions are answered there.
I finished mine and gotta say it's totally worth it. Dayum.
There is a complete crate 4.6 on ebay as well..... $2900.
I would take the valve cover off first and check the followers as mentioned before in here... that might be the problem, and if it is, just do a PI head swap and be dome with it.